Nothing
inst/tests/src/corradoFluxLists.R
In SoilR: Models of Soil Organic Matter Decomposition
#
# vim:set ff=unix expandtab ts=2 sw=2:
# |C_am | |X_01|
# |C_as | |X_02|
# |C_bm | |X_03|
# |C_bs | |X_04|
# |C_fw | |X_05|
# |C_acw| |X_06|
# |C_bcw| |X_07|
# |C_mic| |X_08|
# |C_slo| |X_09|
# X = |C_pas| = |X_10|
# |N_am | |X_11|
# |N_as | |X_12|
# |N_bm | |X_13|
# |N_bs | |X_14|
# |N_fw | |X_15|
# |N_acw| |X_16|
# |N_bcw| |X_17|
# |N_mic| |X_18|
# |N_slo| |X_19|
# |N_pas| |X_20|
# |N_ino| |X_21|
# Call functions to simulate CN fluxes
source("functions_corrado.R")
# Internal fluxes
internal_fluxes = list()
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Carbon fluxes # ----
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Flux from Abovegr. Metabolic to Surface Microbial SOM
internal_fluxes[["C_am->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# C:N ratio of new material entering Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural to Surface Microbial SOM
internal_fluxes[["C_as->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural to Slow SOM
internal_fluxes[["C_as->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Metabolic to Microbial SOM
internal_fluxes[["C_bm->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bm
n_cont = N_bm
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural to Microbial SOM
internal_fluxes[["C_bs->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural to Slow SOM
internal_fluxes[["C_bs->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
}
# Flux from Fine Wood to Surface Microbial SOM
internal_fluxes[["C_fw->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
}
# Flux from Fine Wood to Slow SOM
internal_fluxes[["C_fw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Coarse Wood to Surface Microbial SOM
internal_fluxes[["C_acw->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Coarse Wood to Slow SOM
internal_fluxes[["C_acw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Coarse Wood to Microbial SOM
internal_fluxes[["C_bcw->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Coarse Wood to Slow SOM
internal_fluxes[["C_bcw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
}
# Flux from Surface Microbial SOM to Slow SOM
internal_fluxes[["C_srfmic->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2 in CENTURY4
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM to Slow SOM
internal_fluxes[["C_mic->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM to Passive SOM
internal_fluxes[["C_mic->C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new = bgdrat(N_ino # rceto3 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
}
# Flux from Slow SOM to Microbial SOM
internal_fluxes[["C_slo->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
}
# Flux from Slow SOM to Passive SOM
internal_fluxes[["C_slo->C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
}
# Flux from Passive SOM to Microbial SOM
internal_fluxes[["C_pas->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
}
# # *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Nitrogen fluxes ----
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Nitrogen Flux from Abovegr. Metabolic to Surface Microbial SOM
internal_fluxes[["N_am->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Transfer Nitrogen flux if N lost from the pool is positive
n_am_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Surface Microbial SOM
internal_fluxes[["N_as->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Transfer Nitrogen flux if N lost from the pool is positive
n_as_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Slow SOM
internal_fluxes[["N_as->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Transfer Nitrogen flux if N lost from the pool is positive
n_as_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Metabolic to Microbial SOM
internal_fluxes[["N_bm->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bm_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Microbial SOM
internal_fluxes[["N_bs->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bs_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Slow SOM
internal_fluxes[["N_bs->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bs_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Fine Wood to Surface Microbial SOM
internal_fluxes[["N_fw->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_fw_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Fine Wood to Slow SOM
internal_fluxes[["N_fw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_fw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Coarse Wood to Surface Microbial SOM
internal_fluxes[["N_acw->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_acw_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Coarse Wood to Slow SOM
internal_fluxes[["N_acw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_acw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Coarse Wood to Microbial SOM
internal_fluxes[["N_bcw->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bcw_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Coarse Wood to Slow SOM
internal_fluxes[["N_bcw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bcw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Surface Microbial SOM to Slow SOM
internal_fluxes[["N_srfmic->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = (c_cont / n_cont) + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_srfmic_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Slow SOM
internal_fluxes[["N_mic->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_mic_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Passive SOM
internal_fluxes[["N_mic->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_mic_to_n_pas <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Slow SOM to Microbial SOM
internal_fluxes[["N_slo->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Transfer Nitrogen flux if N lost from the pool is positive
n_slo_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Slow SOM to Passive SOM
internal_fluxes[["N_slo->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Transfer Nitrogen flux if N lost from the pool is positive
n_slo_to_n_pas <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Passive SOM to Microbial SOM
internal_fluxes[["N_pas->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Transfer Nitrogen flux if N lost from the pool is positive
n_pas_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Mineralization fluxes ----
# Nitrogen Flux from Abovegr. Metabolic to Inorganic Nitrogen
internal_fluxes[["N_am->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Mineralized Nitrogen
n_am_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Inorganic Nitrogen
internal_fluxes[["N_as->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS --> SRF MIC
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Mineralized Nitrogen
n_as_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# AS --> SLO
# ***************
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Mineralized Nitrogen
n_as_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_as_to_n_ino = n_as_to_n_ino_1 + n_as_to_n_ino_2
}
# Nitrogen Flux from Belowgr. Metabolic to Inorganic Nitrogen
internal_fluxes[["N_bm->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Mineralized Nitrogen
n_bm_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Inorganic Nitrogen
internal_fluxes[["N_bs->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BS --> MIC
# ***************
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Mineralized Nitrogen
n_bs_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# BS --> SLO
# ***************
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Mineralized Nitrogen
n_bs_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_bs_to_n_ino = n_bs_to_n_ino_1 + n_bs_to_n_ino_2
}
# Nitrogen Flux from Fine Wood to Inorganic Nitrogen
internal_fluxes[["N_fw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# FW --> SRF MIC
# ***************
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Mineralized Nitrogen
n_fw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# FW --> SLO
# ***************
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Mineralized Nitrogen
n_fw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_fw_to_n_ino = n_fw_to_n_ino_1 + n_fw_to_n_ino_2
}
# Nitrogen Flux from Abovegr. Coarse Wood to Inorganic Nitrogen
internal_fluxes[["N_acw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# ACW --> SRF MIC
# ***************
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Mineralized Nitrogen
n_acw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# ACW --> SLO
# ***************
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Mineralized Nitrogen
n_acw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_acw_to_n_ino = n_acw_to_n_ino_1 + n_acw_to_n_ino_2
}
# Nitrogen Flux from Belowgr. Coarse Wood to Inorganic Nitrogen
internal_fluxes[["N_bcw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BCW --> MIC
# ***************
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Mineralized Nitrogen
n_bcw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# BCW --> SLO
# ***************
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Mineralized Nitrogen
n_bcw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_bcw_to_n_ino = n_bcw_to_n_ino_1 + n_bcw_to_n_ino_2
}
# Nitrogen Flux from Surface Microbial SOM to Inorganic Nitrogen
internal_fluxes[["N_srfmic->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Mineralized Nitrogen
n_srfmic_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Inorganic Nitrogen
internal_fluxes[["N_mic->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# MIC --> SLO
# ***************
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Mineralized Nitrogen
n_mic_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# MIC --> PAS
# ***************
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Mineralized Nitrogen
n_mic_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_mic_to_n_ino = n_mic_to_n_ino_1 + n_mic_to_n_ino_2
}
# Nitrogen Flux from Slow SOM to Inorganic Nitrogen
internal_fluxes[["N_slo->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# SLO --> MIC
# ***************
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Mineralized Nitrogen
n_slo_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# SLO --> PAS
# ***************
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Mineralized Nitrogen
n_slo_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_slo_to_n_ino = n_slo_to_n_ino_1 + n_slo_to_n_ino_2
}
# Nitrogen Flux from Passive SOM to Inorganic Nitrogen
internal_fluxes[["N_pas->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Mineralized Nitrogen
n_pas_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Immobilization ----
# Nitrogen Flux from Inorganic Nitrogen to Surface Microbial SOM
internal_fluxes[["N_ino->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AM
# ******
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Immobilized Nitrogen
n_ino_to_n_srfmic_1 <- immob_n(c_transf, outofa, cn_rat_new)
# AS
# ******
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Immobilized Nitrogen
n_ino_to_n_srfmic_2 <- immob_n(c_transf, outofa, cn_rat_new)
# FW
# ******
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Immobilized Nitrogen
n_ino_to_n_srfmic_3 <- immob_n(c_transf, outofa, cn_rat_new)
# ACW
# ******
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Immobilized Nitrogen
n_ino_to_n_srfmic_4 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_srfmic = n_ino_to_n_srfmic_1 + n_ino_to_n_srfmic_2 + n_ino_to_n_srfmic_3 + n_ino_to_n_srfmic_4
}
# Nitrogen Flux from Inorganic Nitrogen to Microbial SOM
internal_fluxes[["N_ino->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BM
# ******
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Immobilized Nitrogen
n_ino_to_n_mic_1 <- immob_n(c_transf, outofa, cn_rat_new)
# BS
# ******
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Immobilized Nitrogen
n_ino_to_n_mic_2 <- immob_n(c_transf, outofa, cn_rat_new)
# BCW
# ******
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Immobilized Nitrogen
n_ino_to_n_mic_3 <- immob_n(c_transf, outofa, cn_rat_new)
# SLO
# ******
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Immobilized Nitrogen
n_ino_to_n_mic_4 <- immob_n(c_transf, outofa, cn_rat_new)
# PAS
# ******
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Immobilized Nitrogen
n_ino_to_n_mic_5 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_mic = n_ino_to_n_mic_1 + n_ino_to_n_mic_2 + n_ino_to_n_mic_3 + n_ino_to_n_mic_4
+ n_ino_to_n_mic_5
}
# Nitrogen Flux from Inorganic Nitrogen to Slow SOM
internal_fluxes[["N_ino->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS
# ******
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Immobilized Nitrogen
n_ino_to_n_slo_1 <- immob_n(c_transf, outofa, cn_rat_new)
# BS
# ******
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Immobilized Nitrogen
n_ino_to_n_slo_2 <- immob_n(c_transf, outofa, cn_rat_new)
# FW
# ******
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Immobilized Nitrogen
n_ino_to_n_slo_3 <- immob_n(c_transf, outofa, cn_rat_new)
# ACW
# ******
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Immobilized Nitrogen
n_ino_to_n_slo_4 <- immob_n(c_transf, outofa, cn_rat_new)
# BCW
# ******
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Immobilized Nitrogen
n_ino_to_n_slo_5 <- immob_n(c_transf, outofa, cn_rat_new)
# SRF MIC
# ******
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Immobilized Nitrogen
n_ino_to_n_slo_6 <- immob_n(c_transf, outofa, cn_rat_new)
# MIC
# ******
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Immobilized Nitrogen
n_ino_to_n_slo_7 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_slo = n_ino_to_n_slo_1 + n_ino_to_n_slo_2 + n_ino_to_n_slo_3 + n_ino_to_n_slo_4
+ n_ino_to_n_slo_5 + n_ino_to_n_slo_6 + n_ino_to_n_slo_7
}
# Nitrogen Flux from Inorganic Nitrogen to Passive SOM
internal_fluxes[["N_ino->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# MIC
# ******
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Immobilized Nitrogen
n_ino_to_n_pas_1 <- immob_n(c_transf, outofa, cn_rat_new)
# SLO
# ******
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Immobilized Nitrogen
n_ino_to_n_pas_2 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_pas = n_ino_to_n_pas_1 + n_ino_to_n_pas_2
}
# Outfluxes ----
out_fluxes = list()
# Flux from Abovegr. Metabolic
out_fluxes[["C_am"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# C:N ratio of new material entering Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_co2 = ifelse(C_am > 0
,ifelse(cando == TRUE
,co2am * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural
out_fluxes[["C_as"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS -> SRF MIC
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_co2_1 = ifelse(C_as > 0
,ifelse(cando == TRUE
,co2as1 * (1 - ligfr_as) * tcflow
,0
)
,0
)
# AS -> SLO
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_co2_2 = ifelse(C_as > 0
,ifelse(cando == TRUE
,co2as2 * ligfr_as * tcflow
,0
)
,0
)
c_as_to_co2 = c_as_to_co2_1 + c_as_to_co2_2
}
# Flux from Belowgr. Metabolic
out_fluxes[["C_bm"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bm
n_cont = N_bm
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_co2 = ifelse(C_bm > 0
,ifelse(cando == TRUE
,co2bm * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural
out_fluxes[["C_bs"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS -> MIC
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_co2_1 = ifelse(C_bs > 0
,ifelse(cando == TRUE
,co2bs1 * (1 - ligfr_bs) * tcflow
,0
)
,0
)
# AS -> SLO
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_co2_2 = ifelse(C_bs > 0
,ifelse(cando == TRUE
,co2bs2 * ligfr_bs * tcflow
,0
)
,0
)
c_bs_to_co2 = c_bs_to_co2_1 + c_bs_to_co2_2
}
# Flux from Fine Wood
out_fluxes[["C_fw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# FW -> SRF MIC
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_co2_1 = ifelse(C_fw > 0
,ifelse(cando == TRUE
,co2fw1 * (1 - ligfr_fw) * tcflow
,0
)
,0
)
# FW -> SLO
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_co2_2 = ifelse(C_fw > 0
,ifelse(cando == TRUE
,co2fw2 * ligfr_fw * tcflow
,0
)
,0
)
c_fw_to_co2 = c_fw_to_co2_1 + c_fw_to_co2_2
}
# Flux from Abovegr. Coarse Wood
out_fluxes[["C_acw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# ACW -> MIC
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_co2_1 = ifelse(C_acw > 0
,ifelse(cando == TRUE
,co2acw1 * (1 - ligfr_acw) * tcflow
,0
)
,0
)
# ACW -> SLO
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_co2_2 = ifelse(C_acw > 0
,ifelse(cando == TRUE
,co2acw2 * ligfr_acw * tcflow
,0
)
,0
)
c_acw_to_co2 = c_acw_to_co2_1 + c_acw_to_co2_2
}
# Flux from Belowgr. Coarse Wood
out_fluxes[["C_bcw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BCW -> MIC
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_co2_1 = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,co2bcw1 * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
# BCW -> SLO
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_co2_2 = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,co2bcw2 * ligfr_bcw * tcflow
,0
)
,0
)
c_bcw_to_co2 = c_bcw_to_co2_1 + c_bcw_to_co2_2
}
# Flux from Surface Microbial SOM
out_fluxes[["C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2 in CENTURY4
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,co2srfmic * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM
out_fluxes[["C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_co2 = ifelse(C_mic > 0
,ifelse(cando == TRUE
,co2mic * tcflow
,0
)
,0
)
}
# Flux from Slow SOM
out_fluxes[["C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_co2 = ifelse(C_slo > 0
,ifelse(cando == TRUE
,co2slo * tcflow
,0
)
,0
)
}
# Flux from Passive SOM
out_fluxes[["C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_co2 = ifelse(C_pas > 0
,ifelse(cando == TRUE
,co2pas * tcflow
,0
)
,0
)
}
# Flux from Aboveground Metabolic Nitrogen
out_fluxes[["N_am"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Aboveground Structural Nitrogen
out_fluxes[["N_as"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Metabolic Nitrogen
out_fluxes[["N_bm"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Structural Nitrogen
out_fluxes[["N_bs"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Fine Wood Nitrogen
out_fluxes[["N_fw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Abovegr. Coarse Wood Nitrogen
out_fluxes[["N_acw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Coarse Wood Nitrogen
out_fluxes[["N_bcw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Microbial SOM Nitrogen
out_fluxes[["N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Microbial SOM Nitrogen
out_fluxes[["N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Slow SOM Nitrogen
out_fluxes[["N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Passive SOM Nitrogen
out_fluxes[["N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Inorganic Nitrogen
out_fluxes[["N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
kup * N_ino
}
# Input fluxes - Constant (Carbon fluxes) ----
input_fluxes_const = list()
# Input C flux into Abovegr. Metabolic Lit
input_fluxes_const[["C_am"]] = function() {
leaf_inp * fm_frac('abg', ligfr_as)
}
# Input C flux into Abovegr. Structural Lit
input_fluxes_const[["C_as"]] = function() {
leaf_inp * (1 - fm_frac('abg', ligfr_as))
}
# Input C flux into Belowgr. Metabolic Lit
input_fluxes_const[["C_bm"]] = function() {
froo_inp * fm_frac('blg', ligfr_bs)
}
# Input C flux into Belowgr. Structural Lit
input_fluxes_const[["C_bs"]] = function() {
froo_inp * (1 - fm_frac('blg', ligfr_bs))
}
# Input C flux into Fine Wood Lit
input_fluxes_const[["C_fw"]] = function() {
fw_inp
}
# Input C flux into Abovegr. Coarse Wood Lit
input_fluxes_const[["C_acw"]] = function() {
acw_inp
}
# Input C flux into Belowgr. Coarse Wood Lit
input_fluxes_const[["C_bcw"]] = function() {
bcw_inp
}
# Input N flux into Abovegr. Metabolic Lit
input_fluxes_const[["N_am"]] = function() {
leaf_inp * fm_frac('abg', ligfr_as) / cn_leaf
}
# Input N flux into Abovegr. Structural Lit
input_fluxes_const[["N_as"]] = function() {
leaf_inp * (1 - fm_frac('abg', ligfr_as)) / cn_leaf
}
# Input N flux into Belowgr. Metabolic Lit
input_fluxes_const[["N_bm"]] = function() {
froo_inp * fm_frac('blg', ligfr_bs) / cn_froo
}
# Input N flux into Belowgr. Structural Lit
input_fluxes_const[["N_bs"]] = function() {
froo_inp * (1 - fm_frac('blg', ligfr_bs)) / cn_froo
}
# Input N flux into Fine Wood Lit
input_fluxes_const[["N_fw"]] = function() {
fw_inp / cn_wood
}
# Input N flux into Abovegr. Coarse Wood Lit
input_fluxes_const[["N_acw"]] = function() {
acw_inp / cn_wood
}
# Input N flux into Belowgr. Coarse Wood Lit
input_fluxes_const[["N_bcw"]] = function() {
bcw_inp / cn_wood
}
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#
# vim:set ff=unix expandtab ts=2 sw=2:
# |C_am | |X_01|
# |C_as | |X_02|
# |C_bm | |X_03|
# |C_bs | |X_04|
# |C_fw | |X_05|
# |C_acw| |X_06|
# |C_bcw| |X_07|
# |C_mic| |X_08|
# |C_slo| |X_09|
# X = |C_pas| = |X_10|
# |N_am | |X_11|
# |N_as | |X_12|
# |N_bm | |X_13|
# |N_bs | |X_14|
# |N_fw | |X_15|
# |N_acw| |X_16|
# |N_bcw| |X_17|
# |N_mic| |X_18|
# |N_slo| |X_19|
# |N_pas| |X_20|
# |N_ino| |X_21|
# Call functions to simulate CN fluxes
source("functions_corrado.R")
# Internal fluxes
internal_fluxes = list()
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Carbon fluxes # ----
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Flux from Abovegr. Metabolic to Surface Microbial SOM
internal_fluxes[["C_am->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# C:N ratio of new material entering Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural to Surface Microbial SOM
internal_fluxes[["C_as->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural to Slow SOM
internal_fluxes[["C_as->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Metabolic to Microbial SOM
internal_fluxes[["C_bm->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bm
n_cont = N_bm
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural to Microbial SOM
internal_fluxes[["C_bs->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural to Slow SOM
internal_fluxes[["C_bs->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
}
# Flux from Fine Wood to Surface Microbial SOM
internal_fluxes[["C_fw->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
}
# Flux from Fine Wood to Slow SOM
internal_fluxes[["C_fw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Coarse Wood to Surface Microbial SOM
internal_fluxes[["C_acw->C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Coarse Wood to Slow SOM
internal_fluxes[["C_acw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Coarse Wood to Microbial SOM
internal_fluxes[["C_bcw->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Coarse Wood to Slow SOM
internal_fluxes[["C_bcw->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
}
# Flux from Surface Microbial SOM to Slow SOM
internal_fluxes[["C_srfmic->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2 in CENTURY4
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM to Slow SOM
internal_fluxes[["C_mic->C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM to Passive SOM
internal_fluxes[["C_mic->C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new = bgdrat(N_ino # rceto3 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
}
# Flux from Slow SOM to Microbial SOM
internal_fluxes[["C_slo->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
}
# Flux from Slow SOM to Passive SOM
internal_fluxes[["C_slo->C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
}
# Flux from Passive SOM to Microbial SOM
internal_fluxes[["C_pas->C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
}
# # *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Nitrogen fluxes ----
# *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
# Nitrogen Flux from Abovegr. Metabolic to Surface Microbial SOM
internal_fluxes[["N_am->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Transfer Nitrogen flux if N lost from the pool is positive
n_am_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Surface Microbial SOM
internal_fluxes[["N_as->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Transfer Nitrogen flux if N lost from the pool is positive
n_as_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Slow SOM
internal_fluxes[["N_as->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Transfer Nitrogen flux if N lost from the pool is positive
n_as_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Metabolic to Microbial SOM
internal_fluxes[["N_bm->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bm_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Microbial SOM
internal_fluxes[["N_bs->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bs_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Slow SOM
internal_fluxes[["N_bs->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bs_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Fine Wood to Surface Microbial SOM
internal_fluxes[["N_fw->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_fw_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Fine Wood to Slow SOM
internal_fluxes[["N_fw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_fw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Coarse Wood to Surface Microbial SOM
internal_fluxes[["N_acw->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_acw_to_n_srfmic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Coarse Wood to Slow SOM
internal_fluxes[["N_acw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_acw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Coarse Wood to Microbial SOM
internal_fluxes[["N_bcw->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bcw_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Coarse Wood to Slow SOM
internal_fluxes[["N_bcw->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Transfer Nitrogen flux if N lost from the pool is positive
n_bcw_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Surface Microbial SOM to Slow SOM
internal_fluxes[["N_srfmic->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = (c_cont / n_cont) + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_srfmic_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Slow SOM
internal_fluxes[["N_mic->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_mic_to_n_slo <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Passive SOM
internal_fluxes[["N_mic->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Transfer Nitrogen flux if N lost from the pool is positive
n_mic_to_n_pas <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Slow SOM to Microbial SOM
internal_fluxes[["N_slo->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Transfer Nitrogen flux if N lost from the pool is positive
n_slo_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Slow SOM to Passive SOM
internal_fluxes[["N_slo->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Transfer Nitrogen flux if N lost from the pool is positive
n_slo_to_n_pas <- esched(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Passive SOM to Microbial SOM
internal_fluxes[["N_pas->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Transfer Nitrogen flux if N lost from the pool is positive
n_pas_to_n_mic <- esched(c_transf, outofa, cn_rat_new)
}
# Mineralization fluxes ----
# Nitrogen Flux from Abovegr. Metabolic to Inorganic Nitrogen
internal_fluxes[["N_am->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Mineralized Nitrogen
n_am_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Abovegr. Structural to Inorganic Nitrogen
internal_fluxes[["N_as->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS --> SRF MIC
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Mineralized Nitrogen
n_as_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# AS --> SLO
# ***************
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Mineralized Nitrogen
n_as_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_as_to_n_ino = n_as_to_n_ino_1 + n_as_to_n_ino_2
}
# Nitrogen Flux from Belowgr. Metabolic to Inorganic Nitrogen
internal_fluxes[["N_bm->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Mineralized Nitrogen
n_bm_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Belowgr. Structural to Inorganic Nitrogen
internal_fluxes[["N_bs->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BS --> MIC
# ***************
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Mineralized Nitrogen
n_bs_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# BS --> SLO
# ***************
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Mineralized Nitrogen
n_bs_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_bs_to_n_ino = n_bs_to_n_ino_1 + n_bs_to_n_ino_2
}
# Nitrogen Flux from Fine Wood to Inorganic Nitrogen
internal_fluxes[["N_fw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# FW --> SRF MIC
# ***************
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Mineralized Nitrogen
n_fw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# FW --> SLO
# ***************
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Mineralized Nitrogen
n_fw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_fw_to_n_ino = n_fw_to_n_ino_1 + n_fw_to_n_ino_2
}
# Nitrogen Flux from Abovegr. Coarse Wood to Inorganic Nitrogen
internal_fluxes[["N_acw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# ACW --> SRF MIC
# ***************
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Mineralized Nitrogen
n_acw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# ACW --> SLO
# ***************
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Mineralized Nitrogen
n_acw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_acw_to_n_ino = n_acw_to_n_ino_1 + n_acw_to_n_ino_2
}
# Nitrogen Flux from Belowgr. Coarse Wood to Inorganic Nitrogen
internal_fluxes[["N_bcw->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BCW --> MIC
# ***************
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Mineralized Nitrogen
n_bcw_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# BCW --> SLO
# ***************
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Mineralized Nitrogen
n_bcw_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_bcw_to_n_ino = n_bcw_to_n_ino_1 + n_bcw_to_n_ino_2
}
# Nitrogen Flux from Surface Microbial SOM to Inorganic Nitrogen
internal_fluxes[["N_srfmic->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Mineralized Nitrogen
n_srfmic_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Nitrogen Flux from Microbial SOM to Inorganic Nitrogen
internal_fluxes[["N_mic->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# MIC --> SLO
# ***************
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Mineralized Nitrogen
n_mic_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# MIC --> PAS
# ***************
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Mineralized Nitrogen
n_mic_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_mic_to_n_ino = n_mic_to_n_ino_1 + n_mic_to_n_ino_2
}
# Nitrogen Flux from Slow SOM to Inorganic Nitrogen
internal_fluxes[["N_slo->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# SLO --> MIC
# ***************
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Mineralized Nitrogen
n_slo_to_n_ino_1 <- mineral_n(c_transf, outofa, cn_rat_new)
# SLO --> PAS
# ***************
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Mineralized Nitrogen
n_slo_to_n_ino_2 <- mineral_n(c_transf, outofa, cn_rat_new)
# Total Mineralized Nitrogen
n_slo_to_n_ino = n_slo_to_n_ino_1 + n_slo_to_n_ino_2
}
# Nitrogen Flux from Passive SOM to Inorganic Nitrogen
internal_fluxes[["N_pas->N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Mineralized Nitrogen
n_pas_to_n_ino <- mineral_n(c_transf, outofa, cn_rat_new)
}
# Immobilization ----
# Nitrogen Flux from Inorganic Nitrogen to Surface Microbial SOM
internal_fluxes[["N_ino->N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AM
# ******
# Compute the C:N ratio of new material entering in Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_c_srfmic = ifelse(C_am > 0
,ifelse(cando == TRUE
,(1 - co2am) * tcflow
,0
)
,0
)
c_transf = c_am_to_c_srfmic
outofa = c_am_to_c_srfmic / (C_am / N_am)
# Immobilized Nitrogen
n_ino_to_n_srfmic_1 <- immob_n(c_transf, outofa, cn_rat_new)
# AS
# ******
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_srfmic = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as1) * (1 - ligfr_as) * tcflow
,0
)
,0
)
c_transf = c_as_to_c_srfmic
outofa = c_as_to_c_srfmic / (C_as / N_as)
# Immobilized Nitrogen
n_ino_to_n_srfmic_2 <- immob_n(c_transf, outofa, cn_rat_new)
# FW
# ******
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_srfmic = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw1) * (1 - ligfr_fw) * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_srfmic
outofa = c_fw_to_c_srfmic / (C_fw / N_fw)
# Immobilized Nitrogen
n_ino_to_n_srfmic_3 <- immob_n(c_transf, outofa, cn_rat_new)
# ACW
# ******
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_srfmic = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw1) * (1 - ligfr_acw) * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_srfmic
outofa = c_acw_to_c_srfmic / (C_acw / N_acw)
# Immobilized Nitrogen
n_ino_to_n_srfmic_4 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_srfmic = n_ino_to_n_srfmic_1 + n_ino_to_n_srfmic_2 + n_ino_to_n_srfmic_3 + n_ino_to_n_srfmic_4
}
# Nitrogen Flux from Inorganic Nitrogen to Microbial SOM
internal_fluxes[["N_ino->N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BM
# ******
c_cont = C_bm
n_cont = N_bm
# C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_mic = ifelse(C_bm > 0
,ifelse(cando == TRUE
,(1 - co2bm) * tcflow
,0
)
,0
)
c_transf = c_bm_to_c_mic
outofa = c_bm_to_c_mic / (C_bm / N_bm)
# Immobilized Nitrogen
n_ino_to_n_mic_1 <- immob_n(c_transf, outofa, cn_rat_new)
# BS
# ******
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_mic = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs1) * (1 - ligfr_bs) * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_mic
outofa = c_bs_to_c_mic / (C_bs / N_bs)
# Immobilized Nitrogen
n_ino_to_n_mic_2 <- immob_n(c_transf, outofa, cn_rat_new)
# BCW
# ******
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_mic = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw1) * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_mic
outofa = c_bcw_to_c_mic / (C_bcw / N_bcw)
# Immobilized Nitrogen
n_ino_to_n_mic_3 <- immob_n(c_transf, outofa, cn_rat_new)
# SLO
# ******
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_mic = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslomic * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_mic
outofa = c_slo_to_c_mic / (C_slo / N_slo)
# Immobilized Nitrogen
n_ino_to_n_mic_4 <- immob_n(c_transf, outofa, cn_rat_new)
# PAS
# ******
c_cont = C_pas
n_cont = N_pas
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_c_mic = ifelse(C_pas > 0
,ifelse(cando == TRUE
,frpasmic * tcflow
,0
)
,0
)
c_transf = c_pas_to_c_mic
outofa = c_pas_to_c_mic / (C_pas / N_pas)
# Immobilized Nitrogen
n_ino_to_n_mic_5 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_mic = n_ino_to_n_mic_1 + n_ino_to_n_mic_2 + n_ino_to_n_mic_3 + n_ino_to_n_mic_4
+ n_ino_to_n_mic_5
}
# Nitrogen Flux from Inorganic Nitrogen to Slow SOM
internal_fluxes[["N_ino->N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS
# ******
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_c_slo = ifelse(C_as > 0
,ifelse(cando == TRUE
,(1 - co2as2) * ligfr_as * tcflow
,0
)
,0
)
c_transf = c_as_to_c_slo
outofa = c_as_to_c_slo / (C_as / N_as)
# Immobilized Nitrogen
n_ino_to_n_slo_1 <- immob_n(c_transf, outofa, cn_rat_new)
# BS
# ******
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_c_slo = ifelse(C_bs > 0
,ifelse(cando == TRUE
,(1 - co2bs2) * ligfr_bs * tcflow
,0
)
,0
)
c_transf = c_bs_to_c_slo
outofa = c_bs_to_c_slo / (C_bs / N_bs)
# Immobilized Nitrogen
n_ino_to_n_slo_2 <- immob_n(c_transf, outofa, cn_rat_new)
# FW
# ******
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_c_slo = ifelse(C_fw > 0
,ifelse(cando == TRUE
,(1 - co2fw2) * ligfr_fw * tcflow
,0
)
,0
)
c_transf = c_fw_to_c_slo
outofa = c_fw_to_c_slo / (C_fw / N_fw)
# Immobilized Nitrogen
n_ino_to_n_slo_3 <- immob_n(c_transf, outofa, cn_rat_new)
# ACW
# ******
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_c_slo = ifelse(C_acw > 0
,ifelse(cando == TRUE
,(1 - co2acw2) * ligfr_acw * tcflow
,0
)
,0
)
c_transf = c_acw_to_c_slo
outofa = c_acw_to_c_slo / (C_acw / N_acw)
# Immobilized Nitrogen
n_ino_to_n_slo_4 <- immob_n(c_transf, outofa, cn_rat_new)
# BCW
# ******
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_c_slo = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,(1 - co2bcw2) * ligfr_bcw * tcflow
,0
)
,0
)
c_transf = c_bcw_to_c_slo
outofa = c_bcw_to_c_slo / (C_bcw / N_bcw)
# Immobilized Nitrogen
n_ino_to_n_slo_5 <- immob_n(c_transf, outofa, cn_rat_new)
# SRF MIC
# ******
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,frsrfmicslo * tcflow
,0
)
,0
)
c_transf = c_srfmic_to_c_slo
outofa = c_srfmic_to_c_slo / (C_srfmic / N_srfmic)
# Immobilized Nitrogen
n_ino_to_n_slo_6 <- immob_n(c_transf, outofa, cn_rat_new)
# MIC
# ******
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino # rceto2
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_slo = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicslo * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_slo
outofa = c_mic_to_c_slo / (C_mic / N_mic)
# Immobilized Nitrogen
n_ino_to_n_slo_7 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_slo = n_ino_to_n_slo_1 + n_ino_to_n_slo_2 + n_ino_to_n_slo_3 + n_ino_to_n_slo_4
+ n_ino_to_n_slo_5 + n_ino_to_n_slo_6 + n_ino_to_n_slo_7
}
# Nitrogen Flux from Inorganic Nitrogen to Passive SOM
internal_fluxes[["N_ino->N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# MIC
# ******
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto3
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_c_pas = ifelse(C_mic > 0
,ifelse(cando == TRUE
,frmicpas * tcflow
,0
)
,0
)
c_transf = c_mic_to_c_pas
outofa = c_mic_to_c_pas / (C_mic / N_mic)
# Immobilized Nitrogen
n_ino_to_n_pas_1 <- immob_n(c_transf, outofa, cn_rat_new)
# SLO
# ******
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat3_1
varatx_2 = varat3_2
varatx_3 = varat3_3
cn_rat_new <- bgdrat(N_ino # rceto
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_c_pas = ifelse(C_slo > 0
,ifelse(cando == TRUE
,frslopas * tcflow
,0
)
,0
)
c_transf = c_slo_to_c_pas
outofa = c_slo_to_c_pas / (C_slo / N_slo)
# Immobilized Nitrogen
n_ino_to_n_pas_2 <- immob_n(c_transf, outofa, cn_rat_new)
# Total Immobilized Nitrogen
n_ino_to_n_pas = n_ino_to_n_pas_1 + n_ino_to_n_pas_2
}
# Outfluxes ----
out_fluxes = list()
# Flux from Abovegr. Metabolic
out_fluxes[["C_am"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# C:N ratio of new material entering Microbial SOM
c_cont = C_am
n_cont = N_am
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_am * xi(t) * C_am
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_am
,tcflow
,C_am
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_am_to_co2 = ifelse(C_am > 0
,ifelse(cando == TRUE
,co2am * tcflow
,0
)
,0
)
}
# Flux from Abovegr. Structural
out_fluxes[["C_as"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS -> SRF MIC
c_cont = C_as
n_cont = N_as
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_co2_1 = ifelse(C_as > 0
,ifelse(cando == TRUE
,co2as1 * (1 - ligfr_as) * tcflow
,0
)
,0
)
# AS -> SLO
c_cont = C_as
n_cont = N_as
cn_rat_new <- rnewas(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_as * xi(t) * C_as * exp(-pligst * ligfr_as)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_as
,tcflow
,C_as
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_as_to_co2_2 = ifelse(C_as > 0
,ifelse(cando == TRUE
,co2as2 * ligfr_as * tcflow
,0
)
,0
)
c_as_to_co2 = c_as_to_co2_1 + c_as_to_co2_2
}
# Flux from Belowgr. Metabolic
out_fluxes[["C_bm"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# Compute the C:N ratio of new material entering Microbial SOM
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bm
n_cont = N_bm
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bm * xi(t) * C_bm * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bm
,tcflow
,C_bm
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bm_to_c_co2 = ifelse(C_bm > 0
,ifelse(cando == TRUE
,co2bm * tcflow
,0
)
,0
)
}
# Flux from Belowgr. Structural
out_fluxes[["C_bs"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# AS -> MIC
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_1
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_co2_1 = ifelse(C_bs > 0
,ifelse(cando == TRUE
,co2bs1 * (1 - ligfr_bs) * tcflow
,0
)
,0
)
# AS -> SLO
# Verify if decomposition can occur (Nitrogen limitations)
c_cont = C_bs
n_cont = N_bs
cn_rat_new = varat1_2
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bs * xi(t) * C_bs * exp(-pligst * ligfr_bs) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bs
,tcflow
,C_bs
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bs_to_co2_2 = ifelse(C_bs > 0
,ifelse(cando == TRUE
,co2bs2 * ligfr_bs * tcflow
,0
)
,0
)
c_bs_to_co2 = c_bs_to_co2_1 + c_bs_to_co2_2
}
# Flux from Fine Wood
out_fluxes[["C_fw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# FW -> SRF MIC
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_co2_1 = ifelse(C_fw > 0
,ifelse(cando == TRUE
,co2fw1 * (1 - ligfr_fw) * tcflow
,0
)
,0
)
# FW -> SLO
c_cont = C_fw
n_cont = N_fw
cn_rat_new <- rneww1_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_fw * xi(t) * C_fw * exp(-pligst * ligfr_fw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_fw
,tcflow
,C_fw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_fw_to_co2_2 = ifelse(C_fw > 0
,ifelse(cando == TRUE
,co2fw2 * ligfr_fw * tcflow
,0
)
,0
)
c_fw_to_co2 = c_fw_to_co2_1 + c_fw_to_co2_2
}
# Flux from Abovegr. Coarse Wood
out_fluxes[["C_acw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# ACW -> MIC
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- agdrat(c_cont
,n_cont
,biocnv_wood
,cemicb
,pcemic1
,pcemic2
,pcemic3
)
if (cn_rat_new < 10 | cn_rat_new > 16) stop('ERROR: cn_rat_new out of range!')
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_co2_1 = ifelse(C_acw > 0
,ifelse(cando == TRUE
,co2acw1 * (1 - ligfr_acw) * tcflow
,0
)
,0
)
# ACW -> SLO
c_cont = C_acw
n_cont = N_acw
cn_rat_new <- rneww2_2(c_cont
,n_cont
,rad1p1
,rad1p2
,rad1p3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_acw * xi(t) * C_acw * exp(-pligst * ligfr_acw)
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_acw
,tcflow
,C_acw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_acw_to_co2_2 = ifelse(C_acw > 0
,ifelse(cando == TRUE
,co2acw2 * ligfr_acw * tcflow
,0
)
,0
)
c_acw_to_co2 = c_acw_to_co2_1 + c_acw_to_co2_2
}
# Flux from Belowgr. Coarse Wood
out_fluxes[["C_bcw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
# BCW -> MIC
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat1_1
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_co2_1 = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,co2bcw1 * (1 - ligfr_bcw) * tcflow
,0
)
,0
)
# BCW -> SLO
c_cont = C_bcw
n_cont = N_bcw
cn_rat_new = varat2_2
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_bcw * xi(t) * C_bcw * exp(-pligst * ligfr_bcw) * anerb
# If decomposed carbon is higher then Carbon amount in the pool
tcflow = ifelse(tcflow <= C_bcw
,tcflow
,C_bcw
)
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_bcw_to_co2_2 = ifelse(C_bcw > 0
,ifelse(cando == TRUE
,co2bcw2 * ligfr_bcw * tcflow
,0
)
,0
)
c_bcw_to_co2 = c_bcw_to_co2_1 + c_bcw_to_co2_2
}
# Flux from Surface Microbial SOM
out_fluxes[["C_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_srfmic
n_cont = N_srfmic
radds1 = rad1p1 + rad1p2 * ((c_cont / n_cont) - pcemic2)
cn_rat_new = c_cont / n_cont + radds1 # rceto2 in CENTURY4
cn_rat_new = max(cn_rat_new, rad1p3)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_srfmic * xi(t) * C_srfmic
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_srfmic_to_c_slo = ifelse(C_srfmic > 0
,ifelse(cando == TRUE
,co2srfmic * tcflow
,0
)
,0
)
}
# Flux from Microbial SOM
out_fluxes[["C_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_mic
n_cont = N_mic
varatx_1 = varat2_1
varatx_2 = varat2_2
varatx_3 = varat2_3
cn_rat_new <- bgdrat(N_ino
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_mic * xi(t) * C_mic * eftext * anerb
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_mic_to_co2 = ifelse(C_mic > 0
,ifelse(cando == TRUE
,co2mic * tcflow
,0
)
,0
)
}
# Flux from Slow SOM
out_fluxes[["C_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_slo * xi(t) * C_slo * anerb
# Respired Carbon flux if C is positive and Nitrogen is not limiting
c_slo_to_co2 = ifelse(C_slo > 0
,ifelse(cando == TRUE
,co2slo * tcflow
,0
)
,0
)
}
# Flux from Passive SOM
out_fluxes[["C_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
c_cont = C_slo
n_cont = N_slo
varatx_1 = varat1_1
varatx_2 = varat1_2
varatx_3 = varat1_3
cn_rat_new <- bgdrat(N_ino # rceto1 in CENTURY4
,varatx_1
,varatx_2
,varatx_3
)
# Verify if decomposition can occur (Nitrogen limitations)
cando = ifelse(sim_type == 'c-only'
,TRUE
,candec(c_cont
,n_cont
,cn_rat_new
,N_ino
)
)
# Carbon lost by the pool
tcflow = k_pas * xi(t) * C_pas * anerb
# Transfer Carbon flux if C is positive and Nitrogen is not limiting
c_pas_to_co2 = ifelse(C_pas > 0
,ifelse(cando == TRUE
,co2pas * tcflow
,0
)
,0
)
}
# Flux from Aboveground Metabolic Nitrogen
out_fluxes[["N_am"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Aboveground Structural Nitrogen
out_fluxes[["N_as"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Metabolic Nitrogen
out_fluxes[["N_bm"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Structural Nitrogen
out_fluxes[["N_bs"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Fine Wood Nitrogen
out_fluxes[["N_fw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Abovegr. Coarse Wood Nitrogen
out_fluxes[["N_acw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Belowgr. Coarse Wood Nitrogen
out_fluxes[["N_bcw"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Microbial SOM Nitrogen
out_fluxes[["N_srfmic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Microbial SOM Nitrogen
out_fluxes[["N_mic"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Slow SOM Nitrogen
out_fluxes[["N_slo"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Passive SOM Nitrogen
out_fluxes[["N_pas"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
0
}
# Flux from Inorganic Nitrogen
out_fluxes[["N_ino"]] = function(
C_am
,N_am
,C_as
,N_as
,C_bm
,N_bm
,C_bs
,N_bs
,C_fw
,N_fw
,C_acw
,N_acw
,C_bcw
,N_bcw
,C_srfmic
,N_srfmic
,C_mic
,N_mic
,C_slo
,N_slo
,C_pas
,N_pas
,N_ino
,t
) {
kup * N_ino
}
# Input fluxes - Constant (Carbon fluxes) ----
input_fluxes_const = list()
# Input C flux into Abovegr. Metabolic Lit
input_fluxes_const[["C_am"]] = function() {
leaf_inp * fm_frac('abg', ligfr_as)
}
# Input C flux into Abovegr. Structural Lit
input_fluxes_const[["C_as"]] = function() {
leaf_inp * (1 - fm_frac('abg', ligfr_as))
}
# Input C flux into Belowgr. Metabolic Lit
input_fluxes_const[["C_bm"]] = function() {
froo_inp * fm_frac('blg', ligfr_bs)
}
# Input C flux into Belowgr. Structural Lit
input_fluxes_const[["C_bs"]] = function() {
froo_inp * (1 - fm_frac('blg', ligfr_bs))
}
# Input C flux into Fine Wood Lit
input_fluxes_const[["C_fw"]] = function() {
fw_inp
}
# Input C flux into Abovegr. Coarse Wood Lit
input_fluxes_const[["C_acw"]] = function() {
acw_inp
}
# Input C flux into Belowgr. Coarse Wood Lit
input_fluxes_const[["C_bcw"]] = function() {
bcw_inp
}
# Input N flux into Abovegr. Metabolic Lit
input_fluxes_const[["N_am"]] = function() {
leaf_inp * fm_frac('abg', ligfr_as) / cn_leaf
}
# Input N flux into Abovegr. Structural Lit
input_fluxes_const[["N_as"]] = function() {
leaf_inp * (1 - fm_frac('abg', ligfr_as)) / cn_leaf
}
# Input N flux into Belowgr. Metabolic Lit
input_fluxes_const[["N_bm"]] = function() {
froo_inp * fm_frac('blg', ligfr_bs) / cn_froo
}
# Input N flux into Belowgr. Structural Lit
input_fluxes_const[["N_bs"]] = function() {
froo_inp * (1 - fm_frac('blg', ligfr_bs)) / cn_froo
}
# Input N flux into Fine Wood Lit
input_fluxes_const[["N_fw"]] = function() {
fw_inp / cn_wood
}
# Input N flux into Abovegr. Coarse Wood Lit
input_fluxes_const[["N_acw"]] = function() {
acw_inp / cn_wood
}
# Input N flux into Belowgr. Coarse Wood Lit
input_fluxes_const[["N_bcw"]] = function() {
bcw_inp / cn_wood
}
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