modified to accomomdate wood sigma

mingkaijiang · Nov 15, 2018 · d2b39ec · d2b39ec
1 parent 634ec8b
commit d2b39ec
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Showing 51 changed files with 108 additions and 94 deletions.
diff --git a/QE_Functions/baseline_CLM/L_constraint_baseline_CLM.R b/QE_Functions/baseline_CLM/L_constraint_baseline_CLM.R
@@ -4,7 +4,7 @@ L_constraint_baseline_CLM_actual <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive pool
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   

diff --git a/QE_Functions/baseline_CLM/M_constraint_baseline_CLM.R b/QE_Functions/baseline_CLM/M_constraint_baseline_CLM.R
@@ -3,8 +3,8 @@ M_constraint_baseline_CLM_actual <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*pass$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*pass$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/baseline_CLM_simplified/L_constraint_CLM_simplified.R b/QE_Functions/baseline_CLM_simplified/L_constraint_CLM_simplified.R
@@ -13,7 +13,7 @@ L_constraint_CLM_simplified <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive, wood, and leaching
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp  

diff --git a/QE_Functions/baseline_CLM_simplified/M_constraint_CLM_simplified.R b/QE_Functions/baseline_CLM_simplified/M_constraint_CLM_simplified.R
@@ -3,8 +3,8 @@ M_constraint_CLM_simplified <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/baseline_model/L_constraint.R b/QE_Functions/baseline_model/L_constraint.R
@@ -13,7 +13,7 @@ L_constraint <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive, wood, and leaching
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   

diff --git a/QE_Functions/baseline_model/M_constraint.R b/QE_Functions/baseline_model/M_constraint.R
@@ -14,8 +14,8 @@ M_constraint <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow  + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/baseline_model/soil_coef.R b/QE_Functions/baseline_model/soil_coef.R
@@ -58,21 +58,28 @@ soil_coef <- function(df, a) {
     omega_af_pass <- mu_f*omega_am_pass + (1-mu_f)*omega_au_pass
     omega_ar_pass <- mu_r*omega_am_pass + (1-mu_r)*omega_av_pass  
 
+    ### burial fraction for wood (omegaw) into passive pool, assuming all wood enters sfc structural pool
+    omega_aw_pass <- omega_au_pass
+
     ### burial fractions for foliage and root into slow pool
     omega_au_slow <- (pus+pas*pua)/det
     omega_av_slow <- (pvs+pas*pva)/det
     omega_am_slow <- (pas*pma)/det
     omega_af_slow <- mu_f*omega_am_slow + (1-mu_f)*omega_au_slow
     omega_ar_slow <- mu_r*omega_am_slow + (1-mu_r)*omega_av_slow
 
+    ### burial fraction for wood (omegaw) into slow pool, assuming all wood enters sfc structural pool
+    omega_aw_slow <- omega_au_slow
+
     ### fraction of foliage and root litter being transferred to active pool
     transfer_fa <- mu_f*pma + (1-mu_f)*psa
     transfer_ra <- mu_r*pma + (1-mu_r)*psa
+    transfer_wa <- psa
 
     ### out df
     ret <- data.frame(decomp_pass, decomp_slow, qq_pass, qq_slow,
-                      omega_af_pass, omega_ar_pass, omega_af_slow, omega_ar_slow, 
-                      transfer_fa, transfer_ra)
+                      omega_af_pass, omega_ar_pass, omega_af_slow, omega_ar_slow, omega_aw_pass, omega_aw_slow,
+                      transfer_fa, transfer_ra, transfer_wa)
 
     return(ret)
 }
diff --git a/QE_Functions/explicit_mineral_model/L_constraint_expl_min.R b/QE_Functions/explicit_mineral_model/L_constraint_expl_min.R
@@ -13,7 +13,7 @@ L_constraint_expl_min <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive, wood, and leaching
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   

diff --git a/QE_Functions/explicit_mineral_model/M_constraint_expl_min.R b/QE_Functions/explicit_mineral_model/M_constraint_expl_min.R
@@ -14,8 +14,8 @@ M_constraint_expl_min <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/n_uptake_root_biomass/L_constraint_root_clm.R b/QE_Functions/n_uptake_root_biomass/L_constraint_root_clm.R
@@ -18,7 +18,7 @@ L_constraint_root_clm <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   
     nburial <- omega_ap*ncp

diff --git a/QE_Functions/n_uptake_root_biomass/L_constraint_root_gday.R b/QE_Functions/n_uptake_root_biomass/L_constraint_root_gday.R
@@ -18,7 +18,7 @@ L_constraint_root_gday <- function(df, a, Nin_L,
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive, wood, and leaching
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   

diff --git a/QE_Functions/n_uptake_root_biomass/L_constraint_root_ocn.R b/QE_Functions/n_uptake_root_biomass/L_constraint_root_ocn.R
@@ -20,7 +20,7 @@ L_constraint_root_ocn <- function(df, a, C_pass, Nin_L) {
 
     # passive pool burial 
     pass <- soil_coef(df, a)
-    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + a$ar*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   
     nwood <- 0 

diff --git a/QE_Functions/n_uptake_root_biomass/M_constraint_root_clm.R b/QE_Functions/n_uptake_root_biomass/M_constraint_root_clm.R
@@ -8,8 +8,8 @@ M_constraint_root_clm <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/n_uptake_root_biomass/M_constraint_root_gday.R b/QE_Functions/n_uptake_root_biomass/M_constraint_root_gday.R
@@ -15,8 +15,8 @@ M_constraint_root_gday <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/n_uptake_root_biomass/M_constraint_root_ocn.R b/QE_Functions/n_uptake_root_biomass/M_constraint_root_ocn.R
@@ -5,8 +5,8 @@ M_constraint_root_ocn <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + a$ar*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + a$ar*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/priming/L_constraint_prim.R b/QE_Functions/priming/L_constraint_prim.R
@@ -15,7 +15,7 @@ L_constraint_prim <- function(df, a, C_pass, Nin_L) {
     pass <- soil_coef(df, a)
 
     # excluding part of root as it's exudation now
-    omega_ap <- a$af*pass$omega_af_pass + (a$ar-a$ar*a$ariz)*pass$omega_ar_pass 
+    omega_ap <- a$af*pass$omega_af_pass + (a$ar-a$ar*a$ariz)*pass$omega_ar_pass + a$aw*pass$omega_aw_pass
 
     # equation for N constraint with passive, wood, and leaching
     U0 <- Nin_L + (1-pass$qq_pass) * pass$decomp_pass * C_pass * ncp   

diff --git a/QE_Functions/priming/M_constraint_no_prim.R b/QE_Functions/priming/M_constraint_no_prim.R
@@ -18,8 +18,8 @@ M_constraint_no_prim <- function(df, a, C_pass, C_slow, Nin_L) {
 
     # passive pool burial 
     s_coef <- soil_coef(df, a)
-    omega_ap <- a$af*s_coef$omega_af_pass + (a$ar-a$ar*a$ariz)*s_coef$omega_ar_pass 
-    omega_as <- a$af*s_coef$omega_af_slow + (a$ar-a$ar*a$ariz)*s_coef$omega_ar_slow 
+    omega_ap <- a$af*s_coef$omega_af_pass + (a$ar-a$ar*a$ariz)*s_coef$omega_ar_pass + a$aw*s_coef$omega_aw_pass
+    omega_as <- a$af*s_coef$omega_af_slow + (a$ar-a$ar*a$ariz)*s_coef$omega_ar_slow + a$aw*s_coef$omega_aw_slow 
 
     # N comes from decomposition of pass and slow pools
     Npass <- (1-s_coef$qq_pass) * s_coef$decomp_pass * C_pass * ncp

diff --git a/QE_Functions/priming/M_constraint_prim.R b/QE_Functions/priming/M_constraint_prim.R
@@ -29,8 +29,8 @@ M_constraint_prim <- function(df, a, C_pass, C_slow, Nin_L) {
             pass <- soil_coef_prim(df[i], a[i,], NPP)
 
             # again, exclude exudation from root allocation
-            omega_ap <- a[i,]$af*pass$omega_af_pass + (a[i,]$ar-a[i,]$ar*a[i,]$ariz)*pass$omega_ar_pass 
-            omega_as <- a[i,]$af*pass$omega_af_slow + (a[i,]$ar-a[i,]$ar*a[i,]$ariz)*pass$omega_ar_slow 
+            omega_ap <- a[i,]$af*pass$omega_af_pass + (a[i,]$ar-a[i,]$ar*a[i,]$ariz)*pass$omega_ar_pass + a[i,]$aw*pass$omega_aw_pass
+            omega_as <- a[i,]$af*pass$omega_af_slow + (a[i,]$ar-a[i,]$ar*a[i,]$ariz)*pass$omega_ar_slow + a[i,]$aw*pass$omega_aw_slow
 
             # Calculate C slow based on exudation and new decomposition values
             C_slow_new <- omega_as*NPP/pass$decomp_slow/(1-pass$qq_slow)*1000.0

diff --git a/QE_Functions/priming/soil_coef_prim.R b/QE_Functions/priming/soil_coef_prim.R
@@ -59,16 +59,23 @@ soil_coef_prim <- function(df, a, in_npp) {
     omega_af_pass <- mu_f*omega_am_pass + (1-mu_f)*omega_au_pass
     omega_ar_pass <- mu_r*omega_am_pass + (1-mu_r)*omega_av_pass  
 
+    ### burial fraction for wood (omegaw) into passive pool, assuming all wood enters sfc structural pool
+    omega_aw_pass <- omega_au_pass
+
     ### burial fractions for foliage and root into slow pool
     omega_au_slow <- (pus+pas*pua)/det
     omega_av_slow <- (pvs+pas*pva)/det
     omega_am_slow <- (pas*pma)/det
     omega_af_slow <- mu_f*omega_am_slow + (1-mu_f)*omega_au_slow
     omega_ar_slow <- mu_r*omega_am_slow + (1-mu_r)*omega_av_slow
 
+    ### burial fraction for wood (omegaw) into slow pool, assuming all wood enters sfc structural pool
+    omega_aw_slow <- omega_au_slow
+
     ### fraction of foliage and root litter being transferred to active pool
     transfer_fa <- mu_f*pma + (1-mu_f)*psa
     transfer_ra <- mu_r*pma + (1-mu_r)*psa
+    transfer_wa <- psa
 
     # calculate the extra C and N input into active SOM,
     # and the gap between what's needed and what's provided
@@ -84,8 +91,8 @@ soil_coef_prim <- function(df, a, in_npp) {
 
     ### out df
     ret <- data.frame(decomp_pass, decomp_slow, decomp_slow_old, qq_pass, qq_slow,
-                      omega_af_pass, omega_ar_pass, omega_af_slow, omega_ar_slow, 
-                      transfer_fa, transfer_ra)
+                      omega_af_pass, omega_ar_pass, omega_af_slow, omega_ar_slow, omega_aw_pass, omega_aw_slow,
+                      transfer_fa, transfer_ra, transfer_wa)
 
     return(ret)
 }
diff --git a/QE_Scripts/Analytical_Run1.1.R b/QE_Scripts/Analytical_Run1.1.R
@@ -39,8 +39,8 @@ Perform_Analytical_Run1.1 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run1.2.R b/QE_Scripts/Analytical_Run1.2.R
@@ -39,8 +39,8 @@ Perform_Analytical_Run1.2 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run1.R b/QE_Scripts/Analytical_Run1.R
@@ -38,8 +38,8 @@ Perform_Analytical_Run1 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run10.R b/QE_Scripts/Analytical_Run10.R
@@ -43,8 +43,8 @@ Perform_Analytical_Run10 <- function(f.flag = 1) {
     s_coef <- soil_coef(df=VL_act_eq$nf, a=a_pot_eq)
 
     ### Get omega
-    omega_ap <- a_pot_eq$af*s_coef$omega_af_pass + a_pot_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_pot_eq$af*s_coef$omega_af_slow + a_pot_eq$ar*s_coef$omega_ar_slow 
+    omega_ap <- a_pot_eq$af*s_coef$omega_af_pass + a_pot_eq$ar*s_coef$omega_ar_pass + a_pot_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_pot_eq$af*s_coef$omega_af_slow + a_pot_eq$ar*s_coef$omega_ar_slow + a_pot_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run101.R b/QE_Scripts/Analytical_Run101.R
@@ -40,8 +40,8 @@ Perform_Analytical_Run101 <- function(f.flag = 1) {
     s_coef <- soil_coef(df=VL_act_eq$nf, a=a_act_eq)
 
     ### Get omega
-    omega_ap <- a_act_eq$af*s_coef$omega_af_pass + a_act_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_act_eq$af*s_coef$omega_af_slow + a_act_eq$ar*s_coef$omega_ar_slow 
+    omega_ap <- a_act_eq$af*s_coef$omega_af_pass + a_act_eq$ar*s_coef$omega_ar_pass + a_act_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_act_eq$af*s_coef$omega_af_slow + a_act_eq$ar*s_coef$omega_ar_slow + a_act_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run11.R b/QE_Scripts/Analytical_Run11.R
@@ -42,8 +42,8 @@ Perform_Analytical_Run11 <- function(f.flag = 1) {
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
 
     ### Get omega
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow 
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass 
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run2.R b/QE_Scripts/Analytical_Run2.R
@@ -38,8 +38,8 @@ Perform_Analytical_Run2 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run3.R b/QE_Scripts/Analytical_Run3.R
@@ -37,8 +37,8 @@ Perform_Analytical_Run3 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run31.R b/QE_Scripts/Analytical_Run31.R
@@ -49,8 +49,8 @@ Perform_Analytical_Run31 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run32.R b/QE_Scripts/Analytical_Run32.R
@@ -49,8 +49,8 @@ Perform_Analytical_Run32 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run33.R b/QE_Scripts/Analytical_Run33.R
@@ -49,8 +49,8 @@ Perform_Analytical_Run33 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2 

diff --git a/QE_Scripts/Analytical_Run34.R b/QE_Scripts/Analytical_Run34.R
@@ -49,8 +49,8 @@ Perform_Analytical_Run34 <- function(f.flag = 1) {
 
     ### calculate soil parameters, e.g. reburial coef.
     s_coef <- soil_coef(df=VL_eq$nf, a=a_eq)
-    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass
-    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow
+    omega_ap <- a_eq$af*s_coef$omega_af_pass + a_eq$ar*s_coef$omega_ar_pass + a_eq$aw*s_coef$omega_aw_pass
+    omega_as <- a_eq$af*s_coef$omega_af_slow + a_eq$ar*s_coef$omega_ar_slow + a_eq$aw*s_coef$omega_aw_slow
 
     ### Get C from very-long term nutrient cycling solution
     ### return in g C m-2