From a0806e156a6e7236ba1dfd4cb4e2de02ebdb6209 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 19 May 2023 14:00:20 -0400
Subject: [PATCH 01/24] Initial commit for new biogenic related options.

---
 input/namelist.canopy      |  1 +
 src/canopy_bioemi_mod.F90  | 20 ++++++----
 src/canopy_calcs.F90       | 76 +++++++++++++++++++-------------------
 src/canopy_canopts_mod.F90 |  1 +
 src/canopy_readnml.F90     |  7 +++-
 5 files changed, 58 insertions(+), 47 deletions(-)

diff --git a/input/namelist.canopy b/input/namelist.canopy
index a07e3417..22f283d8 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -30,6 +30,7 @@
   lu_opt     =  1
   z0_opt     =  0
   bio_cce    =  0.21
+  bio_vert   =  0
   lai_thresh =  0.1
   frt_thresh =  0.1
   fch_thresh =  0.5
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index 85da7d7c..e3af371c 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -6,7 +6,7 @@ module canopy_bioemi_mod
 
 !:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
     SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
-        TEMP2, LU_OPT, VTYPE, MODRES, CCE, EMI_IND, EMI_OUT)
+        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, EMI_IND, EMI_OUT)
 
 !-----------------------------------------------------------------------
 
@@ -52,6 +52,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),    INTENT( IN )       :: MODRES          ! Canopy model input vertical resolution (m)
         REAL(RK),    INTENT( IN )       :: CCE             ! MEGAN Canopy environment coefficient.
         INTEGER,     INTENT( IN )       :: EMI_IND         ! Input biogenic emissions index
+        INTEGER,     INTENT( IN )       :: VERT            ! MEGAN vertical integration option (default = 0/no integration)
         REAL(RK),    INTENT( OUT )      :: EMI_OUT(:)      ! Output canopy layer volume emissions (kg m-3 s-1)
 
 ! Local Variables
@@ -300,13 +301,16 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
 ! Calculate emissions profile in the canopy
         EMI_OUT = 0.0_rk  ! set initial emissions profile to zero
-        do i=1, SIZE(ZK)
-            if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then  ! above ground level and at/below canopy top
-                FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
-                EMI_OUT(i) = FLAI(i) * EF * GammaTLEAF_AVE(i) * GammaPPFD_AVE(i) * CCE  ! (ug m-3 hr-1)
-                EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk !TBD:  convert emissions output to (kg m-3 s-1)
-            end if
-        end do
+
+        if (VERT .eq. 0) then  !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration
+            do i=1, SIZE(ZK)
+                if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then  ! above ground level and at/below canopy top
+                    FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
+                    EMI_OUT(i) = FLAI(i) * EF * GammaTLEAF_AVE(i) * GammaPPFD_AVE(i) * CCE  ! (ug m-3 hr-1)
+                    EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk !TBD:  convert emissions output to (kg m-3 s-1)
+                end if
+            end do
+        end if
 
     END SUBROUTINE CANOPY_BIO
 
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 3f47929b..8638d8b6 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -153,79 +153,79 @@ SUBROUTINE canopy_calcs
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 1, emi_isop_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 1, emi_isop_3d(i,j,:))
                                     !MYRC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 2, emi_myrc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 2, emi_myrc_3d(i,j,:))
                                     !SABI
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 3, emi_sabi_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 3, emi_sabi_3d(i,j,:))
                                     !LIMO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 4, emi_limo_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 4, emi_limo_3d(i,j,:))
                                     !CARE
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 5, emi_care_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 5, emi_care_3d(i,j,:))
                                     !OCIM
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 6, emi_ocim_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 6, emi_ocim_3d(i,j,:))
                                     !BPIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 7, emi_bpin_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 7, emi_bpin_3d(i,j,:))
                                     !APIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 8, emi_apin_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 8, emi_apin_3d(i,j,:))
                                     !MONO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 9, emi_mono_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 9, emi_mono_3d(i,j,:))
                                     !FARN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 10, emi_farn_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 10, emi_farn_3d(i,j,:))
                                     !CARY
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 11, emi_cary_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 11, emi_cary_3d(i,j,:))
                                     !SESQ
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 12, emi_sesq_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 12, emi_sesq_3d(i,j,:))
                                     !MBOL
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 13, emi_mbol_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 13, emi_mbol_3d(i,j,:))
                                     !METH
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 14, emi_meth_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 14, emi_meth_3d(i,j,:))
                                     !ACET
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 15, emi_acet_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 15, emi_acet_3d(i,j,:))
                                     !CO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 16, emi_co_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 16, emi_co_3d(i,j,:))
                                     !BIDI VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 17, emi_bvoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 17, emi_bvoc_3d(i,j,:))
                                     !Stress VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 18, emi_svoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 18, emi_svoc_3d(i,j,:))
                                     !Other VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, 19, emi_ovoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 19, emi_ovoc_3d(i,j,:))
                                 end if
                             end if
 
@@ -365,79 +365,79 @@ SUBROUTINE canopy_calcs
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 1, emi_isop(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 1, emi_isop(loc,:))
                                 !MYRC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 2, emi_myrc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 2, emi_myrc(loc,:))
                                 !SABI
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 3, emi_sabi(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 3, emi_sabi(loc,:))
                                 !LIMO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 4, emi_limo(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 4, emi_limo(loc,:))
                                 !CARE
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 5, emi_care(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 5, emi_care(loc,:))
                                 !OCIM
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 6, emi_ocim(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 6, emi_ocim(loc,:))
                                 !BPIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 7, emi_bpin(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 7, emi_bpin(loc,:))
                                 !APIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 8, emi_apin(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 8, emi_apin(loc,:))
                                 !MONO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 9, emi_mono(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 9, emi_mono(loc,:))
                                 !FARN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 10, emi_farn(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 10, emi_farn(loc,:))
                                 !CARY
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 11, emi_cary(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 11, emi_cary(loc,:))
                                 !SESQ
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 12, emi_sesq(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 12, emi_sesq(loc,:))
                                 !MBOL
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 13, emi_mbol(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 13, emi_mbol(loc,:))
                                 !METH
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 14, emi_meth(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 14, emi_meth(loc,:))
                                 !ACET
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 15, emi_acet(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 15, emi_acet(loc,:))
                                 !CO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 16, emi_co(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 16, emi_co(loc,:))
                                 !BIDI VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 17, emi_bvoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 17, emi_bvoc(loc,:))
                                 !Stress VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 18, emi_svoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 18, emi_svoc(loc,:))
                                 !Other VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, 19, emi_ovoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 19, emi_ovoc(loc,:))
                             end if
                         end if
 
diff --git a/src/canopy_canopts_mod.F90 b/src/canopy_canopts_mod.F90
index 2fd44171..19b8681e 100644
--- a/src/canopy_canopts_mod.F90
+++ b/src/canopy_canopts_mod.F90
@@ -33,5 +33,6 @@ MODULE canopy_canopts_mod
     real(rk)            ::    z0ghc       !ratio of ground roughness length to canopy top height
     real(rk)            ::    lambdars    !Value representing influence of roughness sublayer (nondimensional)
     real(rk)            ::    bio_cce     !MEGAN biogenic emission canopy environment coefficient.
+    integer             ::    bio_vert    !MEGAN vertical integration of emissions option (default = 0, off)
 
 END MODULE canopy_canopts_mod
diff --git a/src/canopy_readnml.F90 b/src/canopy_readnml.F90
index a9eb4f4a..860cc8b1 100644
--- a/src/canopy_readnml.F90
+++ b/src/canopy_readnml.F90
@@ -23,7 +23,7 @@ SUBROUTINE canopy_readnml
     NAMELIST /userdefs/  infmt_opt, nlat, nlon, modlays, modres, href_opt, href_set, &
         z0ghc, lambdars, flameh_opt, flameh_set, frp_fac, ifcanwind, ifcanwaf, &
         ifcaneddy, ifcanphot, ifcanbio, pai_opt, pai_set, lu_opt, z0_opt, dx_opt, &
-        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce
+        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert
 
 !-------------------------------------------------------------------------------
 ! Error, warning, and informational messages.
@@ -201,6 +201,11 @@ SUBROUTINE canopy_readnml
     bio_cce = 0.21_rk
 !-------------------------------------------------------------------------------
 
+!-------------------------------------------------------------------------------
+! Set default integer value for MEGAN vertical integration of emissions (0, off full leaf-level emissions)
+    bio_vert = 0
+!-------------------------------------------------------------------------------
+
 !-------------------------------------------------------------------------------
 ! Read namelist to get user definitions.  Rewind namelist file after each
 ! read in case namelists are not in the correct order in the namelist.

From 570037a7d94e3aefadb7d3076fc826df39f7fe97 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 19 May 2023 22:48:03 -0400
Subject: [PATCH 02/24] Forced bio_vert option to only default =0 right now...

---
 README.md                 | 1 +
 src/canopy_bioemi_mod.F90 | 9 ++++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 409f0e3e..8f173613 100644
--- a/README.md
+++ b/README.md
@@ -197,6 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
+| `bio_vert`      | user set biogenic vertical integration option (default = 0/no integration, full leaf-level biogenic emissions)         |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
 | `fch_thresh`    | user-set real value of canopy height  threshold for contiguous canopy (m)          |
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index e3af371c..a2ae27d8 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -302,14 +302,17 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 ! Calculate emissions profile in the canopy
         EMI_OUT = 0.0_rk  ! set initial emissions profile to zero
 
-        if (VERT .eq. 0) then  !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration
+        if (VERT .eq. 0) then  !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration)
             do i=1, SIZE(ZK)
-                if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then  ! above ground level and at/below canopy top
+                if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then           ! above ground level and at/below canopy top
                     FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
                     EMI_OUT(i) = FLAI(i) * EF * GammaTLEAF_AVE(i) * GammaPPFD_AVE(i) * CCE  ! (ug m-3 hr-1)
-                    EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk !TBD:  convert emissions output to (kg m-3 s-1)
+                    EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk    !convert emissions output to (kg m-3 s-1)
                 end if
             end do
+        else                   !Need to add vertical sum/ave/integ options here...
+            write(*,*)  'Wrong BIO_VERT choice of ', VERT, ' in namelist...exiting'
+            call exit(2)
         end if
 
     END SUBROUTINE CANOPY_BIO

From cf5275fdb6efbd42f53c74436953e5cbec2e6b1b Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Mon, 22 May 2023 16:15:04 -0400
Subject: [PATCH 03/24] Added new bio_vert=1 option for MEGANv3-like sum.

---
 README.md                 |  2 +-
 src/canopy_bioemi_mod.F90 | 15 ++++++++++++---
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 8f173613..b1840d28 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical integration option (default = 0/no integration, full leaf-level biogenic emissions)         |
+| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only  )         |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
 | `fch_thresh`    | user-set real value of canopy height  threshold for contiguous canopy (m)          |
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index a2ae27d8..7c2d33d0 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -93,10 +93,11 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK) :: E_OPT(SIZE(ZK))                ! maximum normalized emission capacity
         REAL(RK) :: TLEAF_OPT(SIZE(ZK))            ! Tleaf at which E_OPT occurs (K)
         REAL(RK) :: FLAI(SIZE(ZK))                 ! Fractional LAI in layer
+        REAL(RK) :: VPGWT(SIZE(ZK))                ! MEGANv3-like in-canopy weighting factor
         REAL(RK) :: CT1                            ! Activation energy (kJ/mol)
         REAL(RK) :: CEO                            ! Empirical coefficient
         REAL(RK) :: EF                             ! Final Mapped Emission factor (EF) (ug/m2 hr)
-        integer i
+        integer i, LAYERS
 
 ! Constant Canopy Parameters
         REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
@@ -302,7 +303,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 ! Calculate emissions profile in the canopy
         EMI_OUT = 0.0_rk  ! set initial emissions profile to zero
 
-        if (VERT .eq. 0) then  !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration)
+        if (VERT .eq. 0) then         !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration)
             do i=1, SIZE(ZK)
                 if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then           ! above ground level and at/below canopy top
                     FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
@@ -310,7 +311,15 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                     EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk    !convert emissions output to (kg m-3 s-1)
                 end if
             end do
-        else                   !Need to add vertical sum/ave/integ options here...
+        else if (VERT .eq. 1) then       !MEGANv3: Add weighted sum of activity coefficients for all canopy layers
+            LAYERS = floor(FCH/MODRES)
+            do i=1,  SIZE(ZK)
+                VPGWT(i) = 1.0_rk/LAYERS !constant weighting factors across depth of canopy
+            end do
+            EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
+                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+            EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
+        else
             write(*,*)  'Wrong BIO_VERT choice of ', VERT, ' in namelist...exiting'
             call exit(2)
         end if

From abbe51ba8e648e0235e9c002245180fde640b80d Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Mon, 22 May 2023 21:32:49 -0400
Subject: [PATCH 04/24] Added new crop_opt to specify crop type heights.

---
 README.md                  |  2 ++
 input/namelist.canopy      |  2 ++
 src/canopy_calcs.F90       | 32 ++++++++++++++++++++++++++++++++
 src/canopy_canopts_mod.F90 |  2 ++
 src/canopy_readnml.F90     | 13 ++++++++++++-
 5 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b1840d28..d4541e7f 100644
--- a/README.md
+++ b/README.md
@@ -198,6 +198,8 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
 | `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only  )         |
+| `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
+| `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) **\*\*\*** |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
 | `fch_thresh`    | user-set real value of canopy height  threshold for contiguous canopy (m)          |
diff --git a/input/namelist.canopy b/input/namelist.canopy
index 22f283d8..f5cdf2aa 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -31,6 +31,8 @@
   z0_opt     =  0
   bio_cce    =  0.21
   bio_vert   =  0
+  crop_opt   =  0
+  crop_set   =  3.0
   lai_thresh =  0.1
   frt_thresh =  0.1
   fch_thresh =  0.5
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 8638d8b6..84be7e5f 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -84,6 +84,22 @@ SUBROUTINE canopy_calcs
                 if (lu_opt .eq. 0 .or. lu_opt .eq. 1 ) then !VIIRS or MODIS
                     if (vtyperef .gt. 0 .and. vtyperef .le. 10 .or. vtyperef .eq. 12) then !VIIRS or MODIS types
 
+! ... check for crop_opt from user namelist
+                        if (vtyperef .eq. 12) then !VIIRS/MODIS crop type
+                            if (crop_opt .eq. 0) then !use GEDI inputs for crop height
+                                hcmref = hcmref
+                            else if (crop_opt .eq. 1) then !user set constant crop height
+                                hcmref = crop_set
+                                !recalculate
+                                zhc         = zk/hcmref
+                                cansublays  = floor(hcmref/modres)
+                            else
+                                write(*,*)  'Wrong CROP_OPT choice of ', crop_opt, &
+                                    ' in namelist...exiting'
+                                call exit(2)
+                            end if
+                        end if
+
 ! ... check for contiguous canopy conditions at each model grid cell
                         if (hcmref .gt. fch_thresh .and. ffracref .gt. frt_thresh &
                             .and. lairef .gt. lai_thresh) then
@@ -296,6 +312,22 @@ SUBROUTINE canopy_calcs
             if (lu_opt .eq. 0 .or. lu_opt .eq. 1 ) then !VIIRS or MODIS
                 if (vtyperef .gt. 0 .and. vtyperef .le. 10 .or. vtyperef .eq. 12) then !VIIRS or MODIS types
 
+! ... check for crop_opt from user namelist
+                    if (vtyperef .eq. 12) then !VIIRS/MODIS crop type
+                        if (crop_opt .eq. 0) then !use GEDI inputs for crop height
+                            hcmref = hcmref
+                        else if (crop_opt .eq. 1) then !user set constant crop height
+                            hcmref = crop_set
+                            !recalculate
+                            zhc         = zk/hcmref
+                            cansublays  = floor(hcmref/modres)
+                        else
+                            write(*,*)  'Wrong CROP_OPT choice of ', crop_opt, &
+                                ' in namelist...exiting'
+                            call exit(2)
+                        end if
+                    end if
+
 ! ... check for contiguous canopy conditions at each model grid cell
                     if (hcmref .gt. fch_thresh .and. ffracref .gt. frt_thresh &
                         .and. lairef .gt. lai_thresh) then
diff --git a/src/canopy_canopts_mod.F90 b/src/canopy_canopts_mod.F90
index 19b8681e..4c141f4d 100644
--- a/src/canopy_canopts_mod.F90
+++ b/src/canopy_canopts_mod.F90
@@ -34,5 +34,7 @@ MODULE canopy_canopts_mod
     real(rk)            ::    lambdars    !Value representing influence of roughness sublayer (nondimensional)
     real(rk)            ::    bio_cce     !MEGAN biogenic emission canopy environment coefficient.
     integer             ::    bio_vert    !MEGAN vertical integration of emissions option (default = 0, off)
+    integer             ::    crop_opt    !Set default integer for crop vegtype option from GEDI or user (default = 0)
+    real(rk)            ::    crop_set    !Set default value for crop vegtype heights used in model (m) (Default = 3 m)
 
 END MODULE canopy_canopts_mod
diff --git a/src/canopy_readnml.F90 b/src/canopy_readnml.F90
index 860cc8b1..a2ad9a34 100644
--- a/src/canopy_readnml.F90
+++ b/src/canopy_readnml.F90
@@ -23,7 +23,8 @@ SUBROUTINE canopy_readnml
     NAMELIST /userdefs/  infmt_opt, nlat, nlon, modlays, modres, href_opt, href_set, &
         z0ghc, lambdars, flameh_opt, flameh_set, frp_fac, ifcanwind, ifcanwaf, &
         ifcaneddy, ifcanphot, ifcanbio, pai_opt, pai_set, lu_opt, z0_opt, dx_opt, &
-        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert
+        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert, &
+        crop_opt, crop_set
 
 !-------------------------------------------------------------------------------
 ! Error, warning, and informational messages.
@@ -206,6 +207,16 @@ SUBROUTINE canopy_readnml
     bio_vert = 0
 !-------------------------------------------------------------------------------
 
+!-------------------------------------------------------------------------------
+! Set default integer for crop vegtype option from GEDI or user (default = 0)
+    crop_opt = 0
+!-------------------------------------------------------------------------------
+
+!-------------------------------------------------------------------------------
+! Set default value for crop vegtype heights used in model (m) (Default = 3 m)
+    crop_set = 3.0_rk
+!-------------------------------------------------------------------------------
+
 !-------------------------------------------------------------------------------
 ! Read namelist to get user definitions.  Rewind namelist file after each
 ! read in case namelists are not in the correct order in the namelist.

From 1735957cf3f5adbec886d984deb7cf7d09c22b44 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Mon, 22 May 2023 21:39:13 -0400
Subject: [PATCH 05/24] Updated README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d4541e7f..3cff4224 100644
--- a/README.md
+++ b/README.md
@@ -199,7 +199,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
 | `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only  )         |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
-| `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) **\*\*\*** |
+| `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
 | `fch_thresh`    | user-set real value of canopy height  threshold for contiguous canopy (m)          |

From e43d32bd5d5cec6c8b75076ad7dff0d3c50698cf Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 23 May 2023 10:53:22 -0400
Subject: [PATCH 06/24] Added bio_vert=2 option for LAD weighted sum.

---
 README.md                 |  2 +-
 src/canopy_bioemi_mod.F90 | 20 +++++++++++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 3cff4224..9b8e3a4b 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only  )         |
+| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but uses LAD weighted activity coefficients from LAD plant distribution function for the sum -- also units of kg/m2/s in topmost model layer)         |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index 7c2d33d0..351ac814 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -300,8 +300,11 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
         GammaPPFD_AVE = (GammaPPFD_SUN*FSUN) + (GammaPPFD_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
 
+
+!        print*, 'FCLAI=',FCLAI
 ! Calculate emissions profile in the canopy
         EMI_OUT = 0.0_rk  ! set initial emissions profile to zero
+        FLAI = 0.0_rk  ! set initial fractional FLAI (LAD) profile to zero
 
         if (VERT .eq. 0) then         !Full 3D leaf-level biogenic emissions (no averaging, summing, or integration)
             do i=1, SIZE(ZK)
@@ -314,7 +317,22 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         else if (VERT .eq. 1) then       !MEGANv3: Add weighted sum of activity coefficients for all canopy layers
             LAYERS = floor(FCH/MODRES)
             do i=1,  SIZE(ZK)
-                VPGWT(i) = 1.0_rk/LAYERS !constant weighting factors across depth of canopy
+                VPGWT(i) = 1.0_rk/LAYERS !MEGANv3: Constant weighting factors across depth of canopy
+            end do
+            EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
+                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+            EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
+        else if (VERT .eq. 2) then       !Use weighting factors normalized to plant distribution shape (FCLAI)
+            LAYERS = floor(FCH/MODRES)
+            do i=1,  SIZE(ZK)
+                if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then
+                    FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
+                end if
+            end do
+            do i=1,  SIZE(ZK)
+                if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then
+                    VPGWT(i) = (FLAI(i))/sum(FLAI(1:LAYERS))
+                end if
             end do
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
                 VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)

From 2df01845ff2fd6320bfece72badfcf3e920c8677 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 23 May 2023 21:05:45 -0400
Subject: [PATCH 07/24] Switched bio_vert option 1 and 2.

---
 README.md                 |  2 +-
 src/canopy_bioemi_mod.F90 | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 9b8e3a4b..39f8f5ed 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of equally weighted activity coefficients acoss all sub-canopy layers, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but uses LAD weighted activity coefficients from LAD plant distribution function for the sum -- also units of kg/m2/s in topmost model layer)         |
+| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the plant distribution function, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but uses equally weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer)         |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index 351ac814..a89c09a8 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -314,15 +314,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                     EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk    !convert emissions output to (kg m-3 s-1)
                 end if
             end do
-        else if (VERT .eq. 1) then       !MEGANv3: Add weighted sum of activity coefficients for all canopy layers
-            LAYERS = floor(FCH/MODRES)
-            do i=1,  SIZE(ZK)
-                VPGWT(i) = 1.0_rk/LAYERS !MEGANv3: Constant weighting factors across depth of canopy
-            end do
-            EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
-                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
-            EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
-        else if (VERT .eq. 2) then       !Use weighting factors normalized to plant distribution shape (FCLAI)
+        else if (VERT .eq. 1) then       !MEGANv3: Use weighting factors normalized to plant distribution shape (FCLAI)
             LAYERS = floor(FCH/MODRES)
             do i=1,  SIZE(ZK)
                 if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then
@@ -337,6 +329,14 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
                 VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
+        else if (VERT .eq. 2) then       !MEGANv3: Add weighted sum of activity coefficients for all canopy layers
+            LAYERS = floor(FCH/MODRES)
+            do i=1,  SIZE(ZK)
+                VPGWT(i) = 1.0_rk/LAYERS !MEGANv3: Constant weighting factors across depth of canopy
+            end do
+            EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
+                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+            EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
         else
             write(*,*)  'Wrong BIO_VERT choice of ', VERT, ' in namelist...exiting'
             call exit(2)

From e229622323992a504e24dd0b8e74348eb9aa1f44 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Thu, 25 May 2023 11:51:08 -0400
Subject: [PATCH 08/24] Added new gaussian bio_vert option, and moved others
 around.

---
 README.md                 |  2 +-
 src/canopy_bioemi_mod.F90 | 46 ++++++++++++++++++++++++++++++++++++---
 2 files changed, 44 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 39f8f5ed..828ebb11 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the plant distribution function, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but uses equally weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer)         |
+| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer          |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index a89c09a8..f0d39efb 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -94,6 +94,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK) :: TLEAF_OPT(SIZE(ZK))            ! Tleaf at which E_OPT occurs (K)
         REAL(RK) :: FLAI(SIZE(ZK))                 ! Fractional LAI in layer
         REAL(RK) :: VPGWT(SIZE(ZK))                ! MEGANv3-like in-canopy weighting factor
+        REAL(RK) :: GAUSS(SIZE(ZK))                ! MEGANv3-like in-canopy gaussian
         REAL(RK) :: CT1                            ! Activation energy (kJ/mol)
         REAL(RK) :: CEO                            ! Empirical coefficient
         REAL(RK) :: EF                             ! Final Mapped Emission factor (EF) (ug/m2 hr)
@@ -314,7 +315,8 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                     EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk    !convert emissions output to (kg m-3 s-1)
                 end if
             end do
-        else if (VERT .eq. 1) then       !MEGANv3: Use weighting factors normalized to plant distribution shape (FCLAI)
+        else if (VERT .eq. 1) then       !"MEGANv3-like": Use weighting factors normalized to plant distribution shape (FCLAI)
+            !across canopy layers
             LAYERS = floor(FCH/MODRES)
             do i=1,  SIZE(ZK)
                 if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then
@@ -326,13 +328,51 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                     VPGWT(i) = (FLAI(i))/sum(FLAI(1:LAYERS))
                 end if
             end do
+!            print*,'--------------'
+!            print*,sum(VPGWT(1:LAYERS))
+!            print*,'--------------'
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
                 VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
-        else if (VERT .eq. 2) then       !MEGANv3: Add weighted sum of activity coefficients for all canopy layers
+        else if (VERT .eq. 2) then       !"MEGANv3-like": Add weighted sum of activity coefficients using normal distribution
+            !across canopy layers using 5 layer numbers directly from MEGANv3
+            !--warning: weights are not consistent with FCLAI distribution
+            !used for biomass distribution used for sunlit/shaded in Gamma TLEAF and GammaPPFD.
+            LAYERS = floor(FCH/MODRES)
+            do i=1, SIZE(ZK)
+                if (ZK(i) .gt. FCH) then
+                    GAUSS(i) = 0.0
+                else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+                    GAUSS(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                        (/ 0.118464_rk,0.0_rk /),ZK(i))
+                else if (ZK(i) .le. FCH*(4.0_rk/5.0_rk) .and. ZK(i) .gt. FCH*(3.0_rk/5.0_rk)) then  !Level 2 - 3
+                    GAUSS(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                        (/ 0.239314_rk,0.118464_rk /),ZK(i))
+                else if (ZK(i) .le. FCH*(3.0_rk/5.0_rk) .and. ZK(i) .gt. FCH*(2.0_rk/5.0_rk)) then  !Level 3 - 4
+                    GAUSS(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                        (/ 0.284444_rk,0.239314_rk /),ZK(i))
+                else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) .and. ZK(i) .gt. FCH*(1.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+                    GAUSS(i)   = interp_linear1_internal((/ FCH*(1.0_rk/5.0_rk),FCH*(2.0_rk/5.0_rk) /), &
+                        (/ 0.239314_rk,0.284444_rk /),ZK(i))
+                else if (ZK(i) .le. FCH*(1.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+                    GAUSS(i)   = interp_linear1_internal((/ ZK(1),FCH*(1.0_rk/5.0_rk) /), &
+                        (/ 0.118464_rk,0.239314_rk /),ZK(i))
+                end if
+            end do
+
+            do i=1, SIZE(ZK)
+                VPGWT(i) = GAUSS(i)/sum(GAUSS(1:LAYERS))
+            end do
+            EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
+                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+            EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
+        else if (VERT .eq. 3) then       !"MEGANv3-like": Add weighted sum of activity coefficients equally
+            !across canopy layers
+            !--warning: weights are not consistent with FCLAI distribution
+            !used for biomass distribution used for sunlit/shaded in Gamma TLEAF and GammaPPFD.
             LAYERS = floor(FCH/MODRES)
             do i=1,  SIZE(ZK)
-                VPGWT(i) = 1.0_rk/LAYERS !MEGANv3: Constant weighting factors across depth of canopy
+                VPGWT(i) = 1.0_rk/LAYERS
             end do
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
                 VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)

From 949f011be741510e5b88ef4a8730377003b7a34c Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Thu, 25 May 2023 12:51:12 -0400
Subject: [PATCH 09/24] Added new shrub/savanna/grass (SSG) user options
 (ssg_opt).

---
 README.md                  |  2 ++
 input/namelist.canopy      |  2 ++
 src/canopy_calcs.F90       | 34 +++++++++++++++++++++++++++++++++-
 src/canopy_canopts_mod.F90 |  2 ++
 src/canopy_readnml.F90     | 12 +++++++++++-
 5 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 828ebb11..fb115be3 100644
--- a/README.md
+++ b/README.md
@@ -198,6 +198,8 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
 | `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer          |
+| `ssg_opt`       | integer for using either input data  (= `0`, default) or user set shrub/savanna/grass (SSG) vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not SSG.  Warning: use of ssg_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates SSG  |
+| `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
diff --git a/input/namelist.canopy b/input/namelist.canopy
index f5cdf2aa..76cfec76 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -31,6 +31,8 @@
   z0_opt     =  0
   bio_cce    =  0.21
   bio_vert   =  0
+  ssg_opt    =  0
+  ssg_set    =  1.0
   crop_opt   =  0
   crop_set   =  3.0
   lai_thresh =  0.1
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 84be7e5f..9bb68b97 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -84,9 +84,25 @@ SUBROUTINE canopy_calcs
                 if (lu_opt .eq. 0 .or. lu_opt .eq. 1 ) then !VIIRS or MODIS
                     if (vtyperef .gt. 0 .and. vtyperef .le. 10 .or. vtyperef .eq. 12) then !VIIRS or MODIS types
 
+! ... check for ssg_opt from user namelist
+                        if (vtyperef .ge. 6 .and. vtyperef .le. 10) then !VIIRS/MODIS shrubs/savannas/grasses (SSG) type
+                            if (ssg_opt .eq. 0) then !use GEDI inputs for SSG heights (not likely captured...)
+                                hcmref = hcmref
+                            else if (ssg_opt .eq. 1) then !user set constant shrubs/savannas/grasslands height
+                                hcmref = ssg_set
+                                !recalculate
+                                zhc         = zk/hcmref
+                                cansublays  = floor(hcmref/modres)
+                            else
+                                write(*,*)  'Wrong SSG_OPT choice of ', ssg_opt, &
+                                    ' in namelist...exiting'
+                                call exit(2)
+                            end if
+                        end if
+
 ! ... check for crop_opt from user namelist
                         if (vtyperef .eq. 12) then !VIIRS/MODIS crop type
-                            if (crop_opt .eq. 0) then !use GEDI inputs for crop height
+                            if (crop_opt .eq. 0) then !use GEDI inputs for crop height (not likely captured...)
                                 hcmref = hcmref
                             else if (crop_opt .eq. 1) then !user set constant crop height
                                 hcmref = crop_set
@@ -312,6 +328,22 @@ SUBROUTINE canopy_calcs
             if (lu_opt .eq. 0 .or. lu_opt .eq. 1 ) then !VIIRS or MODIS
                 if (vtyperef .gt. 0 .and. vtyperef .le. 10 .or. vtyperef .eq. 12) then !VIIRS or MODIS types
 
+! ... check for ssg_opt from user namelist
+                    if (vtyperef .ge. 6 .and. vtyperef .le. 10) then !VIIRS/MODIS shrubs/savannas/grasses (SSG) type
+                        if (ssg_opt .eq. 0) then !use GEDI inputs for SSG heights (not likely captured...)
+                            hcmref = hcmref
+                        else if (ssg_opt .eq. 1) then !user set constant shrubs/savannas/grasslands height
+                            hcmref = ssg_set
+                            !recalculate
+                            zhc         = zk/hcmref
+                            cansublays  = floor(hcmref/modres)
+                        else
+                            write(*,*)  'Wrong SSG_OPT choice of ', ssg_opt, &
+                                ' in namelist...exiting'
+                            call exit(2)
+                        end if
+                    end if
+
 ! ... check for crop_opt from user namelist
                     if (vtyperef .eq. 12) then !VIIRS/MODIS crop type
                         if (crop_opt .eq. 0) then !use GEDI inputs for crop height
diff --git a/src/canopy_canopts_mod.F90 b/src/canopy_canopts_mod.F90
index 4c141f4d..55346b99 100644
--- a/src/canopy_canopts_mod.F90
+++ b/src/canopy_canopts_mod.F90
@@ -34,6 +34,8 @@ MODULE canopy_canopts_mod
     real(rk)            ::    lambdars    !Value representing influence of roughness sublayer (nondimensional)
     real(rk)            ::    bio_cce     !MEGAN biogenic emission canopy environment coefficient.
     integer             ::    bio_vert    !MEGAN vertical integration of emissions option (default = 0, off)
+    integer             ::    ssg_opt     !Set default integer for shrubs/savanna/grassland vegtype option from GEDI or user (default = 0)
+    real(rk)            ::    ssg_set     !Set default value for shrubs/savanna/grassland vegtype heights used in model (m) (Default = 1 m)
     integer             ::    crop_opt    !Set default integer for crop vegtype option from GEDI or user (default = 0)
     real(rk)            ::    crop_set    !Set default value for crop vegtype heights used in model (m) (Default = 3 m)
 
diff --git a/src/canopy_readnml.F90 b/src/canopy_readnml.F90
index a2ad9a34..37c649a2 100644
--- a/src/canopy_readnml.F90
+++ b/src/canopy_readnml.F90
@@ -24,7 +24,7 @@ SUBROUTINE canopy_readnml
         z0ghc, lambdars, flameh_opt, flameh_set, frp_fac, ifcanwind, ifcanwaf, &
         ifcaneddy, ifcanphot, ifcanbio, pai_opt, pai_set, lu_opt, z0_opt, dx_opt, &
         dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert, &
-        crop_opt, crop_set
+        ssg_opt, ssg_set, crop_opt, crop_set
 
 !-------------------------------------------------------------------------------
 ! Error, warning, and informational messages.
@@ -207,6 +207,16 @@ SUBROUTINE canopy_readnml
     bio_vert = 0
 !-------------------------------------------------------------------------------
 
+!-------------------------------------------------------------------------------
+! Set default integer for shrubs/savanaa/grasslands vegtype option from GEDI or user (default = 0)
+    ssg_opt = 0
+!-------------------------------------------------------------------------------
+
+!-------------------------------------------------------------------------------
+! Set default value for shrubs/savanaa/grasslands vegtype heights used in model (m) (Default = 1 m)
+    ssg_set = 1.0_rk
+!-------------------------------------------------------------------------------
+
 !-------------------------------------------------------------------------------
 ! Set default integer for crop vegtype option from GEDI or user (default = 0)
     crop_opt = 0

From 2307fb9c11d6637e0bf5fc8c66bbfde07da2c923 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 30 May 2023 22:07:53 -0400
Subject: [PATCH 10/24] Added new CO2 inhibition factor (co2_opt) for biogenic
 emissions.

---
 README.md                  |   2 +
 input/namelist.canopy      |   2 +
 src/canopy_bioemi_mod.F90  |  29 +++++---
 src/canopy_calcs.F90       | 114 ++++++++++++++++++++-----------
 src/canopy_canopts_mod.F90 |   2 +
 src/canopy_readnml.F90     |  12 +++-
 src/canopy_utils_mod.F90   | 133 ++++++++++++++++++++++++++++++++++++-
 7 files changed, 243 insertions(+), 51 deletions(-)

diff --git a/README.md b/README.md
index fb115be3..17c32109 100644
--- a/README.md
+++ b/README.md
@@ -202,6 +202,8 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
+| `co2_opt`       | integer for using different options for the co2 inhibition option for biogenic isoprene emissions using either Possell & Hewitt (2011) (= `0`, default) or Wilkinson et al. (2009) method (= `1`). To turn off co2 inhibition use `co2_opt=2`  |
+| `co2_set`       | user-set real value of atmospheric co2 concentration (ppmv) (only used if `co2_opt=0` or `co2_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
 | `fch_thresh`    | user-set real value of canopy height  threshold for contiguous canopy (m)          |
diff --git a/input/namelist.canopy b/input/namelist.canopy
index 76cfec76..69ffd68a 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -35,6 +35,8 @@
   ssg_set    =  1.0
   crop_opt   =  0
   crop_set   =  3.0
+  co2_opt    =  0
+  co2_set    =  400.0
   lai_thresh =  0.1
   frt_thresh =  0.1
   fch_thresh =  0.5
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index f0d39efb..bc331566 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -6,7 +6,8 @@ module canopy_bioemi_mod
 
 !:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
     SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
-        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, EMI_IND, EMI_OUT)
+        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
+        EMI_IND, EMI_OUT)
 
 !-----------------------------------------------------------------------
 
@@ -32,7 +33,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 !-----------------------------------------------------------------------
 !-----------------------------------------------------------------------
         use canopy_const_mod, ONLY: rk,rgasuniv   !constants for canopy models
-        use canopy_utils_mod,  ONLY: interp_linear1_internal
+        use canopy_utils_mod,  ONLY: interp_linear1_internal, GET_GAMMA_CO2
         use canopy_phot_mod
         use canopy_bioparm_mod
 
@@ -51,8 +52,10 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         INTEGER,     INTENT( IN )       :: VTYPE           ! Grid cell dominant vegetation type
         REAL(RK),    INTENT( IN )       :: MODRES          ! Canopy model input vertical resolution (m)
         REAL(RK),    INTENT( IN )       :: CCE             ! MEGAN Canopy environment coefficient.
-        INTEGER,     INTENT( IN )       :: EMI_IND         ! Input biogenic emissions index
         INTEGER,     INTENT( IN )       :: VERT            ! MEGAN vertical integration option (default = 0/no integration)
+        INTEGER,     INTENT( IN )       :: CO2OPT          ! Option for co2 inhibition calculation
+        REAL(RK),    INTENT( IN )       :: CO2SET          ! User set atmospheric CO2 conc [ppmv]
+        INTEGER,     INTENT( IN )       :: EMI_IND         ! Input biogenic emissions index
         REAL(RK),    INTENT( OUT )      :: EMI_OUT(:)      ! Output canopy layer volume emissions (kg m-3 s-1)
 
 ! Local Variables
@@ -98,6 +101,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK) :: CT1                            ! Activation energy (kJ/mol)
         REAL(RK) :: CEO                            ! Empirical coefficient
         REAL(RK) :: EF                             ! Final Mapped Emission factor (EF) (ug/m2 hr)
+        REAL(RK) :: GAMMACO2                       ! CO2 inhibition factor (isoprene only)
         integer i, LAYERS
 
 ! Constant Canopy Parameters
@@ -301,8 +305,14 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
         GammaPPFD_AVE = (GammaPPFD_SUN*FSUN) + (GammaPPFD_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
 
+! Get CO2 inhibition factor for isoprene only
+
+        if (EMI_IND .eq. 1) then  !Isoprene
+            GAMMACO2 = GET_GAMMA_CO2(CO2OPT,CO2SET)
+        else
+            GAMMACO2 = 1.0_rk
+        end if
 
-!        print*, 'FCLAI=',FCLAI
 ! Calculate emissions profile in the canopy
         EMI_OUT = 0.0_rk  ! set initial emissions profile to zero
         FLAI = 0.0_rk  ! set initial fractional FLAI (LAD) profile to zero
@@ -311,7 +321,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
             do i=1, SIZE(ZK)
                 if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then           ! above ground level and at/below canopy top
                     FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)
-                    EMI_OUT(i) = FLAI(i) * EF * GammaTLEAF_AVE(i) * GammaPPFD_AVE(i) * CCE  ! (ug m-3 hr-1)
+                    EMI_OUT(i) = FLAI(i) * EF * GammaTLEAF_AVE(i) * GammaPPFD_AVE(i) * GAMMACO2 * CCE  ! (ug m-3 hr-1)
                     EMI_OUT(i) = EMI_OUT(i) * 2.7777777777778E-13_rk    !convert emissions output to (kg m-3 s-1)
                 end if
             end do
@@ -328,11 +338,8 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                     VPGWT(i) = (FLAI(i))/sum(FLAI(1:LAYERS))
                 end if
             end do
-!            print*,'--------------'
-!            print*,sum(VPGWT(1:LAYERS))
-!            print*,'--------------'
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
-                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+                VPGWT(1:LAYERS)) * GAMMACO2 * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
         else if (VERT .eq. 2) then       !"MEGANv3-like": Add weighted sum of activity coefficients using normal distribution
             !across canopy layers using 5 layer numbers directly from MEGANv3
@@ -364,7 +371,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                 VPGWT(i) = GAUSS(i)/sum(GAUSS(1:LAYERS))
             end do
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
-                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+                VPGWT(1:LAYERS)) * GAMMACO2 * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
         else if (VERT .eq. 3) then       !"MEGANv3-like": Add weighted sum of activity coefficients equally
             !across canopy layers
@@ -375,7 +382,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                 VPGWT(i) = 1.0_rk/LAYERS
             end do
             EMI_OUT(SIZE(ZK)) = LAI * EF * SUM(GammaTLEAF_AVE(1:LAYERS) * GammaPPFD_AVE(1:LAYERS) * &
-                VPGWT(1:LAYERS)) * CCE   !put into top model layer (ug m-2 hr-1)
+                VPGWT(1:LAYERS)) * GAMMACO2 * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
         else
             write(*,*)  'Wrong BIO_VERT choice of ', VERT, ' in namelist...exiting'
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 9bb68b97..6c788d1e 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -185,79 +185,98 @@ SUBROUTINE canopy_calcs
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 1, emi_isop_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        1, emi_isop_3d(i,j,:))
                                     !MYRC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 2, emi_myrc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        2, emi_myrc_3d(i,j,:))
                                     !SABI
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 3, emi_sabi_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        3, emi_sabi_3d(i,j,:))
                                     !LIMO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 4, emi_limo_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        4, emi_limo_3d(i,j,:))
                                     !CARE
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 5, emi_care_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        5, emi_care_3d(i,j,:))
                                     !OCIM
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 6, emi_ocim_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        6, emi_ocim_3d(i,j,:))
                                     !BPIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 7, emi_bpin_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        7, emi_bpin_3d(i,j,:))
                                     !APIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 8, emi_apin_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        8, emi_apin_3d(i,j,:))
                                     !MONO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 9, emi_mono_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        9, emi_mono_3d(i,j,:))
                                     !FARN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 10, emi_farn_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        10, emi_farn_3d(i,j,:))
                                     !CARY
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 11, emi_cary_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        11, emi_cary_3d(i,j,:))
                                     !SESQ
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 12, emi_sesq_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        12, emi_sesq_3d(i,j,:))
                                     !MBOL
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 13, emi_mbol_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        13, emi_mbol_3d(i,j,:))
                                     !METH
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 14, emi_meth_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        14, emi_meth_3d(i,j,:))
                                     !ACET
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 15, emi_acet_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        15, emi_acet_3d(i,j,:))
                                     !CO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 16, emi_co_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        16, emi_co_3d(i,j,:))
                                     !BIDI VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 17, emi_bvoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        17, emi_bvoc_3d(i,j,:))
                                     !Stress VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 18, emi_svoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        18, emi_svoc_3d(i,j,:))
                                     !Other VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, 19, emi_ovoc_3d(i,j,:))
+                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        19, emi_ovoc_3d(i,j,:))
                                 end if
                             end if
 
@@ -429,79 +448,98 @@ SUBROUTINE canopy_calcs
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 1, emi_isop(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    1, emi_isop(loc,:))
                                 !MYRC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 2, emi_myrc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    2, emi_myrc(loc,:))
                                 !SABI
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 3, emi_sabi(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    3, emi_sabi(loc,:))
                                 !LIMO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 4, emi_limo(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    4, emi_limo(loc,:))
                                 !CARE
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 5, emi_care(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    5, emi_care(loc,:))
                                 !OCIM
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 6, emi_ocim(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    6, emi_ocim(loc,:))
                                 !BPIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 7, emi_bpin(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    7, emi_bpin(loc,:))
                                 !APIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 8, emi_apin(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    8, emi_apin(loc,:))
                                 !MONO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 9, emi_mono(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    9, emi_mono(loc,:))
                                 !FARN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 10, emi_farn(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    10, emi_farn(loc,:))
                                 !CARY
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 11, emi_cary(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    11, emi_cary(loc,:))
                                 !SESQ
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 12, emi_sesq(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    12, emi_sesq(loc,:))
                                 !MBOL
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 13, emi_mbol(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    13, emi_mbol(loc,:))
                                 !METH
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 14, emi_meth(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    14, emi_meth(loc,:))
                                 !ACET
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 15, emi_acet(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    15, emi_acet(loc,:))
                                 !CO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 16, emi_co(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    16, emi_co(loc,:))
                                 !BIDI VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 17, emi_bvoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    17, emi_bvoc(loc,:))
                                 !Stress VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 18, emi_svoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    18, emi_svoc(loc,:))
                                 !Other VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, 19, emi_ovoc(loc,:))
+                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    19, emi_ovoc(loc,:))
                             end if
                         end if
 
diff --git a/src/canopy_canopts_mod.F90 b/src/canopy_canopts_mod.F90
index 55346b99..028002a4 100644
--- a/src/canopy_canopts_mod.F90
+++ b/src/canopy_canopts_mod.F90
@@ -38,5 +38,7 @@ MODULE canopy_canopts_mod
     real(rk)            ::    ssg_set     !Set default value for shrubs/savanna/grassland vegtype heights used in model (m) (Default = 1 m)
     integer             ::    crop_opt    !Set default integer for crop vegtype option from GEDI or user (default = 0)
     real(rk)            ::    crop_set    !Set default value for crop vegtype heights used in model (m) (Default = 3 m)
+    integer             ::    co2_opt     !Set default integer for co2 inhibition option for biogenic isoprene emissions (default=0; Possell & Hewitt (2011))
+    real(rk)            ::    co2_set     !Set default value for atmospheric co2 concentration for co2_opt (m) (Default = 400.0 ppmv)
 
 END MODULE canopy_canopts_mod
diff --git a/src/canopy_readnml.F90 b/src/canopy_readnml.F90
index 37c649a2..f92a1abb 100644
--- a/src/canopy_readnml.F90
+++ b/src/canopy_readnml.F90
@@ -24,7 +24,7 @@ SUBROUTINE canopy_readnml
         z0ghc, lambdars, flameh_opt, flameh_set, frp_fac, ifcanwind, ifcanwaf, &
         ifcaneddy, ifcanphot, ifcanbio, pai_opt, pai_set, lu_opt, z0_opt, dx_opt, &
         dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert, &
-        ssg_opt, ssg_set, crop_opt, crop_set
+        ssg_opt, ssg_set, crop_opt, crop_set, co2_opt, co2_set
 
 !-------------------------------------------------------------------------------
 ! Error, warning, and informational messages.
@@ -227,6 +227,16 @@ SUBROUTINE canopy_readnml
     crop_set = 3.0_rk
 !-------------------------------------------------------------------------------
 
+!-------------------------------------------------------------------------------
+! Set default integer for co2 inhibition option for biogenic isoprene emissions (default = 0; Possell & Hewitt (2011))
+    co2_opt = 0
+!-------------------------------------------------------------------------------
+
+!-------------------------------------------------------------------------------
+! Set default value for atmospheric co2 concentration for co2_opt (m) (Default = 400.0 ppmv)
+    co2_set = 400.0_rk
+!-------------------------------------------------------------------------------
+
 !-------------------------------------------------------------------------------
 ! Read namelist to get user definitions.  Rewind namelist file after each
 ! read in case namelists are not in the correct order in the namelist.
diff --git a/src/canopy_utils_mod.F90 b/src/canopy_utils_mod.F90
index 312f07a3..a87d8fa0 100644
--- a/src/canopy_utils_mod.F90
+++ b/src/canopy_utils_mod.F90
@@ -6,7 +6,7 @@ module canopy_utils_mod
 
     private
     public IntegrateTrapezoid,interp_linear1_internal,CalcPAI, &
-        CalcDX,CalcFlameH
+        CalcDX,CalcFlameH,GET_GAMMA_CO2
 
 contains
 
@@ -125,4 +125,135 @@ function CalcFlameH(frp, dx)
 
     end function
 
+    real(rk) function GET_GAMMA_CO2(co2_opt, co2_set)  result( GAMMA_CO2 )
+        !!------------------------------------------------------------------------------
+        !                   Harmonized Emissions Component (HEMCO)                    !
+        !------------------------------------------------------------------------------
+        !BOP
+        !
+        ! !IROUTINE: get_gamma_co2
+        !
+        ! !DESCRIPTION: Function GET\_GAMMA\_CO2 computes the CO2 activity factor
+        !  associated with CO2 inhibition of isoprene emission. Called from
+        !  GET\_MEGAN\_EMISSIONS only.
+        !\\
+        !\\
+        ! !INTERFACE:
+
+        ! !INPUT PARAMETERS:
+        integer,  INTENT(IN) :: co2_opt       ! Option for co2 inhibition calculation
+        ! 0=Possell & Hewitt (2011);
+        ! 1=Wilkinson et al. (2009)
+        ! >1=off
+        real(rk), INTENT(IN) :: co2_set       ! User set atmospheric CO2 conc [ppmv]
+        !
+        ! !RETURN VALUE:
+!        REAL(rk)             :: GAMMA_CO2  ! CO2 activity factor [unitless]
+        !
+        ! !LOCAL VARIABLES:
+        REAL(rk)             :: CO2i       ! Intercellular CO2 conc [ppmv]
+        REAL(rk)             :: ISMAXi     ! Asymptote for intercellular CO2
+        REAL(rk)             :: HEXPi      ! Exponent for intercellular CO2
+        REAL(rk)             :: CSTARi     ! Scaling coef for intercellular CO2
+        REAL(rk)             :: ISMAXa     ! Asymptote for atmospheric CO2
+        REAL(rk)             :: HEXPa      ! Exponent for atmospheric CO2
+        REAL(rk)             :: CSTARa     ! Scaling coef for atmospheric CO2
+        !
+        ! !REMARKS:
+        !  References:
+        !  ============================================================================
+        !  (1 ) Heald, C. L., Wilkinson, M. J., Monson, R. K., Alo, C. A.,
+        !       Wang, G. L., and Guenther, A.: Response of isoprene emission
+        !       to ambient co(2) changes and implications for global budgets,
+        !       Global Change Biology, 15, 1127-1140, 2009.
+        !  (2 ) Wilkinson, M. J., Monson, R. K., Trahan, N., Lee, S., Brown, E.,
+        !       Jackson, R. B., Polley, H. W., Fay, P. A., and Fall, R.: Leaf
+        !       isoprene emission rate as a function of atmospheric CO2
+        !       concentration, Global Change Biology, 15, 1189-1200, 2009.
+        !  (3 ) Possell, M., and Hewitt, C. N.: Isoprene emissions from plants
+        !       are mediated by atmospheric co2 concentrations, Global Change
+        !       Biology, 17, 1595-1610, 2011.
+
+        ! !REVISION HISTORY:
+        !  (1 ) Implemented in the standard code by A. Tai (Jun 2012).
+        !  See https://github.com/geoschem/hemco for complete history
+        !EOP
+        !------------------------------------------------------------------------------
+        !BOC
+
+        !-----------------------
+        ! Compute GAMMA_CO2
+        !-----------------------
+
+        !----------------------------------------------------------
+        ! Choose between two alternative CO2 inhibition schemes
+        !----------------------------------------------------------
+
+        IF ( co2_opt .eq. 0 ) THEN
+
+            ! Use empirical relationship of Possell & Hewitt (2011):
+            ! Empirical relationship of Possell & Hewitt (2011) based on nine
+            ! experimental studies including Wilkinson et al. (2009). This is
+            ! especially recommended for sub-ambient CO2 concentrations:
+
+            GAMMA_CO2 = 8.9406_rk / ( 1.0_rk + 8.9406_rk * 0.0024_rk * co2_set )
+
+
+        ELSEIF ( co2_opt .eq. 1 ) THEN
+
+            ! Use parameterization of Wilkinson et al. (2009):
+            ! Semi-process-based parameterization of Wilkinson et al. (2009),
+            ! taking into account of sensitivity to intercellular CO2
+            ! fluctuation, which is here set as a constant fraction of
+            ! atmospheric CO2:
+
+
+            ! Parameters for intercellular CO2 using linear interpolation:
+            IF ( co2_set <= 600.0_rk ) THEN
+                ISMAXi = 1.036_rk  - (1.036_rk - 1.072_rk) / &
+                    (600.0_rk - 400.0_rk) * (600.0_rk - co2_set)
+                HEXPi  = 2.0125_rk - (2.0125_rk - 1.7000_rk) / &
+                    (600.0_rk - 400.0_rk) * (600.0_rk - co2_set)
+                CSTARi = 1150.0_rk - (1150.0_rk - 1218.0_rk) / &
+                    (600.0_rk - 400.0_rk) * (600.0_rk - co2_set)
+            ELSEIF ( co2_set > 600.0_rk .AND. co2_set < 800.0_rk ) THEN
+                ISMAXi = 1.046_rk  - (1.046_rk - 1.036_rk) / &
+                    (800.0_rk - 600.0_rk) * (800.0_rk - co2_set)
+                HEXPi  = 1.5380_rk - (1.5380_rk - 2.0125_rk) / &
+                    (800.0_rk - 600.0_rk) * (800.0_rk - co2_set)
+                CSTARi = 2025.0_rk - (2025.0_rk - 1150.0_rk) / &
+                    (800.0_rk - 600.0_rk) * (800.0_rk - co2_set)
+            ELSE
+                ISMAXi = 1.014_rk - (1.014_rk - 1.046_rk) / &
+                    (1200.0_rk - 800.0_rk) * (1200.0_rk - co2_set)
+                HEXPi  = 2.8610_rk - (2.8610_rk - 1.5380_rk) / &
+                    (1200.0_rk - 800.0_rk) * (1200.0_rk - co2_set)
+                CSTARi = 1525.0_rk - (1525.0_rk - 2025.0_rk) / &
+                    (1200.0_rk - 800.0_rk) * (1200.0_rk - co2_set)
+            ENDIF
+
+            ! Parameters for atmospheric CO2:
+            ISMAXa    = 1.344_rk
+            HEXPa     = 1.4614_rk
+            CSTARa    = 585.0_rk
+
+            ! For now, set CO2_Ci = 0.7d0 * CO2_Ca as recommended by Heald
+            ! et al. (2009):
+            CO2i      = 0.7_rk * co2_set
+
+            ! Compute GAMMA_CO2:
+            GAMMA_CO2 = ( ISMAXi -  ISMAXi * CO2i**HEXPi / &
+                ( CSTARi**HEXPi + CO2i**HEXPi ) )  &
+                * ( ISMAXa - ISMAXa * ( 0.7_rk * co2_set )**HEXPa / &
+                ( CSTARa**HEXPa + ( 0.7_rk * co2_set )**HEXPa ) )
+
+        ELSE
+
+            ! No CO2 inhibition scheme is used; GAMMA_CO2 set to unity:
+            GAMMA_CO2 = 1.0_rk
+
+        ENDIF
+
+    end function GET_GAMMA_CO2
+
 end module canopy_utils_mod

From f12a839e854467a6a2f71676fcd5145f826ce052 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 30 May 2023 22:10:29 -0400
Subject: [PATCH 11/24] Updated README.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 17c32109..5b113096 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
-| `co2_opt`       | integer for using different options for the co2 inhibition option for biogenic isoprene emissions using either Possell & Hewitt (2011) (= `0`, default) or Wilkinson et al. (2009) method (= `1`). To turn off co2 inhibition use `co2_opt=2`  |
+| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the Possell & Hewitt (2011) (= `0`, default) or Wilkinson et al. (2009) method (= `1`). To turn off co2 inhibition factor set `co2_opt=2`  |
 | `co2_set`       | user-set real value of atmospheric co2 concentration (ppmv) (only used if `co2_opt=0` or `co2_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |

From 7060b6b3ecbcb245cbe4ad2bb6fcda2318cdee79 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 30 May 2023 22:16:21 -0400
Subject: [PATCH 12/24] Updated README.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5b113096..97e29311 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
-| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the Possell & Hewitt (2011) (= `0`, default) or Wilkinson et al. (2009) method (= `1`). To turn off co2 inhibition factor set `co2_opt=2`  |
+| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the [Possell & Hewitt (2011)](https://doi.org/10.1111/j.1365-2486.2010.02306.x) (= `0`, default) or [Wilkinson et al. (2009)](https://doi.org/10.1111/j.1365-2486.2008.01803.x) method (= `1`). To turn off co2 inhibition factor set `co2_opt=2`  |
 | `co2_set`       | user-set real value of atmospheric co2 concentration (ppmv) (only used if `co2_opt=0` or `co2_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |

From e89dc13bda8563ced442ebb029b973bf2139d360 Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Thu, 1 Jun 2023 09:22:06 -0400
Subject: [PATCH 13/24] Update README.md

Co-authored-by: Zachary Moon <zachary.moon@noaa.gov>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 97e29311..a6d504be 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg/m2/s and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg/m2/s in topmost model layer          |
+| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg m-2 s-1 and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer          |
 | `ssg_opt`       | integer for using either input data  (= `0`, default) or user set shrub/savanna/grass (SSG) vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not SSG.  Warning: use of ssg_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates SSG  |
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |

From 888eea2d5661237218183c2c3dedd9970e7bb28d Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Thu, 1 Jun 2023 09:24:12 -0400
Subject: [PATCH 14/24] Removed HEMCO header.

---
 src/canopy_utils_mod.F90 | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/canopy_utils_mod.F90 b/src/canopy_utils_mod.F90
index a87d8fa0..f1225174 100644
--- a/src/canopy_utils_mod.F90
+++ b/src/canopy_utils_mod.F90
@@ -126,11 +126,6 @@ function CalcFlameH(frp, dx)
     end function
 
     real(rk) function GET_GAMMA_CO2(co2_opt, co2_set)  result( GAMMA_CO2 )
-        !!------------------------------------------------------------------------------
-        !                   Harmonized Emissions Component (HEMCO)                    !
-        !------------------------------------------------------------------------------
-        !BOP
-        !
         ! !IROUTINE: get_gamma_co2
         !
         ! !DESCRIPTION: Function GET\_GAMMA\_CO2 computes the CO2 activity factor

From 38c59dd312d453bfb9aa61545e770d06c81c145d Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 2 Jun 2023 10:16:16 -0400
Subject: [PATCH 15/24] Update src/canopy_bioemi_mod.F90

Co-authored-by: Zachary Moon <zachary.moon@noaa.gov>
---
 src/canopy_bioemi_mod.F90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index bc331566..fd9013bf 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -327,7 +327,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
             end do
         else if (VERT .eq. 1) then       !"MEGANv3-like": Use weighting factors normalized to plant distribution shape (FCLAI)
             !across canopy layers
-            LAYERS = floor(FCH/MODRES)
+            LAYERS = floor(FCH/MODRES) + 1
             do i=1,  SIZE(ZK)
                 if (ZK(i) .gt. 0.0 .and. ZK(i) .le. FCH) then
                     FLAI(i) = ((FCLAI(i+1) - FCLAI(i)) * LAI)/MODRES    !fractional LAI in each layer converted to LAD (m2 m-3)

From 1c6481f7bb78b4bf9b797e769a14de530f4ca54b Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 2 Jun 2023 12:44:09 -0400
Subject: [PATCH 16/24] Added LAYERS+1 for all bio_vert options for summing.

---
 src/canopy_bioemi_mod.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index fd9013bf..80416083 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -345,7 +345,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
             !across canopy layers using 5 layer numbers directly from MEGANv3
             !--warning: weights are not consistent with FCLAI distribution
             !used for biomass distribution used for sunlit/shaded in Gamma TLEAF and GammaPPFD.
-            LAYERS = floor(FCH/MODRES)
+            LAYERS = floor(FCH/MODRES) + 1
             do i=1, SIZE(ZK)
                 if (ZK(i) .gt. FCH) then
                     GAUSS(i) = 0.0
@@ -377,7 +377,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
             !across canopy layers
             !--warning: weights are not consistent with FCLAI distribution
             !used for biomass distribution used for sunlit/shaded in Gamma TLEAF and GammaPPFD.
-            LAYERS = floor(FCH/MODRES)
+            LAYERS = floor(FCH/MODRES) + 1
             do i=1,  SIZE(ZK)
                 VPGWT(i) = 1.0_rk/LAYERS
             end do

From a42c9a858e847bb589436a723fa14c8dd4c5f2f2 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 2 Jun 2023 16:41:53 -0400
Subject: [PATCH 17/24] Updated README for co2_inhibition warning.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a6d504be..80107377 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
-| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the [Possell & Hewitt (2011)](https://doi.org/10.1111/j.1365-2486.2010.02306.x) (= `0`, default) or [Wilkinson et al. (2009)](https://doi.org/10.1111/j.1365-2486.2008.01803.x) method (= `1`). To turn off co2 inhibition factor set `co2_opt=2`  |
+| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the [Possell & Hewitt (2011)](https://doi.org/10.1111/j.1365-2486.2010.02306.x) (= `0`, default) or [Wilkinson et al. (2009)](https://doi.org/10.1111/j.1365-2486.2008.01803.x) method (= `1`). Use of option = `0` (Possell & Hewitt 2011) is especially recommended for sub-ambient CO2 concentrations.  To turn off co2 inhibition factor set `co2_opt=2`  |
 | `co2_set`       | user-set real value of atmospheric co2 concentration (ppmv) (only used if `co2_opt=0` or `co2_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |

From fb6c4e7fe34432461bdf1df020b68ad2de597d0e Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Sun, 4 Jun 2023 12:49:48 -0400
Subject: [PATCH 18/24] Updated README for co2 inhibition note.

---
 README.md                | 2 +-
 src/canopy_utils_mod.F90 | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 80107377..df4c2ffe 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
 | `crop_set`      | user-set real value of constant crop vegetation type heights (m) (only used if `crop_opt=1`) |
-| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the [Possell & Hewitt (2011)](https://doi.org/10.1111/j.1365-2486.2010.02306.x) (= `0`, default) or [Wilkinson et al. (2009)](https://doi.org/10.1111/j.1365-2486.2008.01803.x) method (= `1`). Use of option = `0` (Possell & Hewitt 2011) is especially recommended for sub-ambient CO2 concentrations.  To turn off co2 inhibition factor set `co2_opt=2`  |
+| `co2_opt`       | user-set options for applying a CO2 inhibition factor for biogenic isoprene-only emissions using either the [Possell & Hewitt (2011)](https://doi.org/10.1111/j.1365-2486.2010.02306.x) (= `0`, default) or [Wilkinson et al. (2009)](https://doi.org/10.1111/j.1365-2486.2008.01803.x) method (= `1`). Use of option = `1` (Possell & Hewitt 2011) is especially recommended for sub-ambient CO2 concentrations.  To turn off co2 inhibition factor set `co2_opt=2`  |
 | `co2_set`       | user-set real value of atmospheric co2 concentration (ppmv) (only used if `co2_opt=0` or `co2_opt=1`) |
 | `lai_thresh`    | user-set real value of LAI threshold for contiguous canopy (m2/m2)                 |
 | `frt_thresh`    | user-set real value of forest fraction threshold for contiguous canopy             |
diff --git a/src/canopy_utils_mod.F90 b/src/canopy_utils_mod.F90
index f1225174..ae1117bb 100644
--- a/src/canopy_utils_mod.F90
+++ b/src/canopy_utils_mod.F90
@@ -188,8 +188,7 @@ real(rk) function GET_GAMMA_CO2(co2_opt, co2_set)  result( GAMMA_CO2 )
 
             ! Use empirical relationship of Possell & Hewitt (2011):
             ! Empirical relationship of Possell & Hewitt (2011) based on nine
-            ! experimental studies including Wilkinson et al. (2009). This is
-            ! especially recommended for sub-ambient CO2 concentrations:
+            ! experimental studies including Wilkinson et al. (2009).
 
             GAMMA_CO2 = 8.9406_rk / ( 1.0_rk + 8.9406_rk * 0.0024_rk * co2_set )
 
@@ -200,7 +199,8 @@ real(rk) function GET_GAMMA_CO2(co2_opt, co2_set)  result( GAMMA_CO2 )
             ! Semi-process-based parameterization of Wilkinson et al. (2009),
             ! taking into account of sensitivity to intercellular CO2
             ! fluctuation, which is here set as a constant fraction of
-            ! atmospheric CO2:
+            ! atmospheric CO2. This is especially recommended for sub-ambient
+            ! CO2 concentrations::
 
 
             ! Parameters for intercellular CO2 using linear interpolation:

From 4d43d2c0cae884045ef269dd4c52f49eb1d0a87f Mon Sep 17 00:00:00 2001
From: zmoon <zmoon92@gmail.com>
Date: Thu, 8 Jun 2023 15:38:21 -0600
Subject: [PATCH 19/24] Add small example comparing the emissions calc opts

for the point case
---
 python/examples.ipynb | 59 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/python/examples.ipynb b/python/examples.ipynb
index d9a75e91..aedd1ac5 100644
--- a/python/examples.ipynb
+++ b/python/examples.ipynb
@@ -760,6 +760,65 @@
     "    ax.plot(clu, ds_c[vn])\n",
     "    ax.set(ylabel=vn, xlabel=\"CLU\")"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "13cc57aa-666c-4f27-ac01-400838ba94a0",
+   "metadata": {},
+   "source": [
+    "### Emissions calculation options"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "578f31ab-832e-4303-88c4-9cb444fe99f9",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "cases = config_cases(\n",
+    "    file_vars=\"../input/input_variables_point.txt\",\n",
+    "    infmt_opt=1,\n",
+    "    nlat=1,\n",
+    "    nlon=1,\n",
+    "    bio_vert=[0, 1, 2],\n",
+    ")\n",
+    "ds = run_config_sens(cases)\n",
+    "ds"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "affd849c-3464-4f27-abc3-1390a4395e31",
+   "metadata": {},
+   "source": [
+    "Currently, method 1 should give the same result as canopy-integrating the laywerwise method 0 results afterwards.\n",
+    "\n",
+    "The method 2 result is smaller since it places more weight on the middle of the canopy, where light levels are lower."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "86b197ac-9ecb-40b2-a7e5-1354fcc0a2d3",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "dz = ds.z.diff(\"z\")\n",
+    "\n",
+    "e0 = float((ds.emi_isop.isel(case=0) * dz).sum(\"z\"))\n",
+    "e1 = float(ds.emi_isop.isel(case=1, z=-1))\n",
+    "e2 = float(ds.emi_isop.isel(case=2, z=-1))\n",
+    "print(e0)\n",
+    "print(e1)\n",
+    "print(e2)\n",
+    "\n",
+    "assert np.isclose(e0, e1)"
+   ]
   }
  ],
  "metadata": {

From 65993eabd2de8f01ef614204866eb142556d5c8c Mon Sep 17 00:00:00 2001
From: zmoon <zmoon92@gmail.com>
Date: Thu, 8 Jun 2023 16:42:23 -0600
Subject: [PATCH 20/24] Add missing emi calc option

---
 python/examples.ipynb | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/python/examples.ipynb b/python/examples.ipynb
index aedd1ac5..d37ba600 100644
--- a/python/examples.ipynb
+++ b/python/examples.ipynb
@@ -783,7 +783,7 @@
     "    infmt_opt=1,\n",
     "    nlat=1,\n",
     "    nlon=1,\n",
-    "    bio_vert=[0, 1, 2],\n",
+    "    bio_vert=[0, 1, 2, 3],\n",
     ")\n",
     "ds = run_config_sens(cases)\n",
     "ds"
@@ -796,7 +796,7 @@
    "source": [
     "Currently, method 1 should give the same result as canopy-integrating the laywerwise method 0 results afterwards.\n",
     "\n",
-    "The method 2 result is smaller since it places more weight on the middle of the canopy, where light levels are lower."
+    "The method 2 result is smaller since it places more weight on the lower--middle regions of the canopy, where light levels are lower. Method 3 is somewhere in between these (consider the shape of the LAD profile vs a Gaussian in height)."
    ]
   },
   {
@@ -813,9 +813,8 @@
     "e0 = float((ds.emi_isop.isel(case=0) * dz).sum(\"z\"))\n",
     "e1 = float(ds.emi_isop.isel(case=1, z=-1))\n",
     "e2 = float(ds.emi_isop.isel(case=2, z=-1))\n",
-    "print(e0)\n",
-    "print(e1)\n",
-    "print(e2)\n",
+    "e3 = float(ds.emi_isop.isel(case=3, z=-1))\n",
+    "print(e0, e1, e2, e3, sep=\"\\n\")\n",
     "\n",
     "assert np.isclose(e0, e1)"
    ]

From c076b6f90b3fc3c4c90567c4e153e73d88f69029 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 9 Jun 2023 14:30:18 -0400
Subject: [PATCH 21/24] Changed bio_vert to biovert_opt to conform NL.

---
 README.md                  |  2 +-
 input/namelist.canopy      | 70 +++++++++++++++++------------------
 src/canopy_bioemi_mod.F90  |  2 +-
 src/canopy_calcs.F90       | 76 +++++++++++++++++++-------------------
 src/canopy_canopts_mod.F90 |  2 +-
 src/canopy_readnml.F90     |  4 +-
 6 files changed, 78 insertions(+), 78 deletions(-)

diff --git a/README.md b/README.md
index df4c2ffe..bd625e92 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `bio_vert`      | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg m-2 s-1 and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer          |
+| `biovert_opt`    user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg m-2 s-1 and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer          |
 | `ssg_opt`       | integer for using either input data  (= `0`, default) or user set shrub/savanna/grass (SSG) vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not SSG.  Warning: use of ssg_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates SSG  |
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |
diff --git a/input/namelist.canopy b/input/namelist.canopy
index 69ffd68a..a51785b9 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -5,39 +5,39 @@
 /
 
 &USERDEFS
-  infmt_opt  =  0
-  nlat       =  43
-  nlon       =  86
-  modlays    =  100
-  modres     =  0.5
-  ifcanwind  = .TRUE.
-  ifcanwaf   = .TRUE.
-  ifcaneddy  = .TRUE.
-  ifcanphot  = .TRUE.
-  ifcanbio   = .TRUE.
-  href_opt   =  0
-  href_set   =  10.0
-  z0ghc      =  0.0025
-  rsl_opt    =  0
-  lambdars   =  1.25
-  dx_opt     =  0
-  dx_set     =  12000.0
-  flameh_opt =  2
-  flameh_set =  1.0
-  frp_fac    =  1.0
-  pai_opt    =  0
-  pai_set    =  4.0
-  lu_opt     =  1
-  z0_opt     =  0
-  bio_cce    =  0.21
-  bio_vert   =  0
-  ssg_opt    =  0
-  ssg_set    =  1.0
-  crop_opt   =  0
-  crop_set   =  3.0
-  co2_opt    =  0
-  co2_set    =  400.0
-  lai_thresh =  0.1
-  frt_thresh =  0.1
-  fch_thresh =  0.5
+  infmt_opt   =  0
+  nlat        =  43
+  nlon        =  86
+  modlays     =  100
+  modres      =  0.5
+  ifcanwind   = .TRUE.
+  ifcanwaf    = .TRUE.
+  ifcaneddy   = .TRUE.
+  ifcanphot   = .TRUE.
+  ifcanbio    = .TRUE.
+  href_opt    =  0
+  href_set    =  10.0
+  z0ghc       =  0.0025
+  rsl_opt     =  0
+  lambdars    =  1.25
+  dx_opt      =  0
+  dx_set      =  12000.0
+  flameh_opt  =  2
+  flameh_set  =  1.0
+  frp_fac     =  1.0
+  pai_opt     =  0
+  pai_set     =  4.0
+  lu_opt      =  1
+  z0_opt      =  0
+  bio_cce     =  0.21
+  biovert_opt =  4
+  ssg_opt     =  0
+  ssg_set     =  1.0
+  crop_opt    =  0
+  crop_set    =  3.0
+  co2_opt     =  0
+  co2_set     =  400.0
+  lai_thresh  =  0.1
+  frt_thresh  =  0.1
+  fch_thresh  =  0.5
 /
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index 80416083..ba3d87d2 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -385,7 +385,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
                 VPGWT(1:LAYERS)) * GAMMACO2 * CCE   !put into top model layer (ug m-2 hr-1)
             EMI_OUT = EMI_OUT * 2.7777777777778E-13_rk    !convert emissions output to    (kg m-2 s-1)
         else
-            write(*,*)  'Wrong BIO_VERT choice of ', VERT, ' in namelist...exiting'
+            write(*,*)  'Wrong BIOVERT_OPT choice of ', VERT, ' in namelist...exiting'
             call exit(2)
         end if
 
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 6c788d1e..e4aef172 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -185,97 +185,97 @@ SUBROUTINE canopy_calcs
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         1, emi_isop_3d(i,j,:))
                                     !MYRC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         2, emi_myrc_3d(i,j,:))
                                     !SABI
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         3, emi_sabi_3d(i,j,:))
                                     !LIMO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         4, emi_limo_3d(i,j,:))
                                     !CARE
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         5, emi_care_3d(i,j,:))
                                     !OCIM
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         6, emi_ocim_3d(i,j,:))
                                     !BPIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         7, emi_bpin_3d(i,j,:))
                                     !APIN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         8, emi_apin_3d(i,j,:))
                                     !MONO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         9, emi_mono_3d(i,j,:))
                                     !FARN
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         10, emi_farn_3d(i,j,:))
                                     !CARY
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         11, emi_cary_3d(i,j,:))
                                     !SESQ
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         12, emi_sesq_3d(i,j,:))
                                     !MBOL
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         13, emi_mbol_3d(i,j,:))
                                     !METH
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         14, emi_meth_3d(i,j,:))
                                     !ACET
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         15, emi_acet_3d(i,j,:))
                                     !CO
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         16, emi_co_3d(i,j,:))
                                     !BIDI VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         17, emi_bvoc_3d(i,j,:))
                                     !Stress VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         18, emi_svoc_3d(i,j,:))
                                     !Other VOC
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                        lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                        lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         19, emi_ovoc_3d(i,j,:))
                                 end if
                             end if
@@ -448,97 +448,97 @@ SUBROUTINE canopy_calcs
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     1, emi_isop(loc,:))
                                 !MYRC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     2, emi_myrc(loc,:))
                                 !SABI
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     3, emi_sabi(loc,:))
                                 !LIMO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     4, emi_limo(loc,:))
                                 !CARE
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     5, emi_care(loc,:))
                                 !OCIM
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     6, emi_ocim(loc,:))
                                 !BPIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     7, emi_bpin(loc,:))
                                 !APIN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     8, emi_apin(loc,:))
                                 !MONO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     9, emi_mono(loc,:))
                                 !FARN
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     10, emi_farn(loc,:))
                                 !CARY
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     11, emi_cary(loc,:))
                                 !SESQ
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     12, emi_sesq(loc,:))
                                 !MBOL
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     13, emi_mbol(loc,:))
                                 !METH
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     14, emi_meth(loc,:))
                                 !ACET
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     15, emi_acet(loc,:))
                                 !CO
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     16, emi_co(loc,:))
                                 !BIDI VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     17, emi_bvoc(loc,:))
                                 !Stress VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     18, emi_svoc(loc,:))
                                 !Other VOC
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
-                                    lu_opt, vtyperef, modres, bio_cce, bio_vert, co2_opt, co2_set, &
+                                    lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     19, emi_ovoc(loc,:))
                             end if
                         end if
diff --git a/src/canopy_canopts_mod.F90 b/src/canopy_canopts_mod.F90
index 028002a4..b3f1c29c 100644
--- a/src/canopy_canopts_mod.F90
+++ b/src/canopy_canopts_mod.F90
@@ -33,7 +33,7 @@ MODULE canopy_canopts_mod
     real(rk)            ::    z0ghc       !ratio of ground roughness length to canopy top height
     real(rk)            ::    lambdars    !Value representing influence of roughness sublayer (nondimensional)
     real(rk)            ::    bio_cce     !MEGAN biogenic emission canopy environment coefficient.
-    integer             ::    bio_vert    !MEGAN vertical integration of emissions option (default = 0, off)
+    integer             ::    biovert_opt    !MEGAN vertical integration of emissions option (default = 0, off)
     integer             ::    ssg_opt     !Set default integer for shrubs/savanna/grassland vegtype option from GEDI or user (default = 0)
     real(rk)            ::    ssg_set     !Set default value for shrubs/savanna/grassland vegtype heights used in model (m) (Default = 1 m)
     integer             ::    crop_opt    !Set default integer for crop vegtype option from GEDI or user (default = 0)
diff --git a/src/canopy_readnml.F90 b/src/canopy_readnml.F90
index f92a1abb..52e63989 100644
--- a/src/canopy_readnml.F90
+++ b/src/canopy_readnml.F90
@@ -23,7 +23,7 @@ SUBROUTINE canopy_readnml
     NAMELIST /userdefs/  infmt_opt, nlat, nlon, modlays, modres, href_opt, href_set, &
         z0ghc, lambdars, flameh_opt, flameh_set, frp_fac, ifcanwind, ifcanwaf, &
         ifcaneddy, ifcanphot, ifcanbio, pai_opt, pai_set, lu_opt, z0_opt, dx_opt, &
-        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, bio_vert, &
+        dx_set, lai_thresh, frt_thresh, fch_thresh, rsl_opt, bio_cce, biovert_opt, &
         ssg_opt, ssg_set, crop_opt, crop_set, co2_opt, co2_set
 
 !-------------------------------------------------------------------------------
@@ -204,7 +204,7 @@ SUBROUTINE canopy_readnml
 
 !-------------------------------------------------------------------------------
 ! Set default integer value for MEGAN vertical integration of emissions (0, off full leaf-level emissions)
-    bio_vert = 0
+    biovert_opt = 0
 !-------------------------------------------------------------------------------
 
 !-------------------------------------------------------------------------------

From 9d61034c95c5d98c06539759fb272cafdab34953 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 9 Jun 2023 14:33:08 -0400
Subject: [PATCH 22/24] Updated NL for biovert_opt = 0 by default

---
 input/namelist.canopy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/input/namelist.canopy b/input/namelist.canopy
index a51785b9..04781010 100755
--- a/input/namelist.canopy
+++ b/input/namelist.canopy
@@ -30,7 +30,7 @@
   lu_opt      =  1
   z0_opt      =  0
   bio_cce     =  0.21
-  biovert_opt =  4
+  biovert_opt =  0
   ssg_opt     =  0
   ssg_set     =  1.0
   crop_opt    =  0

From d3e74202268f8f57dd16b133b9ab802f553e1f76 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 9 Jun 2023 14:34:17 -0400
Subject: [PATCH 23/24] Fixed README for biovert_opt.

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index bd625e92..f3ba4ed7 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022
 | `lu_opt`        | integer for input model land use type (`0`: VIIRS 17 Cat (default) or `1`: MODIS-IGBP 20 Cat (valid LU types 1-10 and 12); input mapped to Massman et al.) |
 | `z0_opt`        | integer (`0`: use model input or `1`: vegtype dependent z0 for first estimate)     |
 | `bio_cce`       | user-set real value of MEGAN biogenic emissions "canopy environment coefficient" used to tune emissions to model inputs/calculations (default: `0.21`, based on Silva et al. 2020) |
-| `biovert_opt`    user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg m-2 s-1 and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer          |
+| `biovert_opt`   | user set biogenic vertical summing option (`0`: no sum, full leaf-level biogenic emissions, units=kg/m3/s; `1`: MEGANv3-like summing of LAD weighted activity coefficients using the canopy-app plant distributions, caution-- units=kg m-2 s-1 and puts the total emissions in the topmost canopy-app model layer only; `2`: Same as in option 1, but instead uses Gaussian/normally weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer; `3`: Same as in option 1, but instead uses evenly weighted activity coefficients acoss all sub-canopy layers -- also units of kg m-2 s-1 in topmost model layer          |
 | `ssg_opt`       | integer for using either input data  (= `0`, default) or user set shrub/savanna/grass (SSG) vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not SSG.  Warning: use of ssg_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates SSG  |
 | `ssg_set`       | user-set real value of constant SSG vegetation type heights (m) (only used if `ssg_opt=1`) |
 | `crop_opt`      | integer for using either input data  (= `0`, default) or user set crop vegetation type heights from namelist (= `1`).  Currently, GEDI FCH input data only provides canopy heights for forests and not crops.  Warning: use of crop_opt=1 will overide typically higher resolution input data (e.g., GEDI) forest canopy heights where the lower resolution vegtype data indicates crops  |

From f851b4ec0de840c802f2cfd736a45dbbfdb1cb11 Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 9 Jun 2023 21:02:44 -0400
Subject: [PATCH 24/24] Update python/examples.ipynb

Co-authored-by: Zachary Moon <zachary.moon@noaa.gov>
---
 python/examples.ipynb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/examples.ipynb b/python/examples.ipynb
index d37ba600..62310959 100644
--- a/python/examples.ipynb
+++ b/python/examples.ipynb
@@ -783,7 +783,7 @@
     "    infmt_opt=1,\n",
     "    nlat=1,\n",
     "    nlon=1,\n",
-    "    bio_vert=[0, 1, 2, 3],\n",
+    "    biovert_opt=[0, 1, 2, 3],\n",
     ")\n",
     "ds = run_config_sens(cases)\n",
     "ds"