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 01/64] 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 02/64] 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 03/64] 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 04/64] 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 05/64] 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 06/64] 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 07/64] 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 08/64] 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 09/64] 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 10/64] 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 11/64] 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 12/64] 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 13/64] 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 14/64] 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 15/64] 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 16/64] 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 17/64] 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 18/64] 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 5824f767e5a97d6f4af8410fee17a7bf306dfc56 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 6 Jun 2023 11:41:28 -0400
Subject: [PATCH 19/64] Initial commit of global python canopy data workflow.

---
 README.md                     |   2 +-
 python/README.md              |  35 +++
 python/environment.yml        |   2 +
 python/global_data_process.py | 431 ++++++++++++++++++++++++++++++++++
 4 files changed, 469 insertions(+), 1 deletion(-)
 create mode 100755 python/global_data_process.py

diff --git a/README.md b/README.md
index 409f0e3e..7ecefac3 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ which is read at runtime.
 ./canopy
 ```
 
-You can also [run with Python](./python/README.md).
+You can also [generate global inputs and run with Python](./python/README.md).
 
 ## Components
 
diff --git a/python/README.md b/python/README.md
index c348d048..06faa58e 100644
--- a/python/README.md
+++ b/python/README.md
@@ -51,3 +51,38 @@ cases = config_cases(
 ds = run_config_sens(cases)
 ```
 :point_up: We still get a single output dataset, but it has a `case` dimension.
+
+:point_down: You can also download and generate global gridded canopy-app inputs using python.
+
+- Edit python script (`global_data_process.py`)
+
+```
+vim global_data_process.py
+```
+
+- Change user settings
+
+```
+'''User Options'''
+path     = '/scratch/pcampbe8/canopy-app/input'    # work directory
+year     = 2022   # year
+month    = 7      # month
+day      = 1      # day
+houri    = 12     # gfs initialization hour in UTC (caution currently GFS files are initialized at 12 UTC only -- do not change)
+hour     = 00     # gfs forecast hour in UTC
+ref_lev  = 10     # reference height (m, a.g.l.)
+frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
+```
+
+- Activate Python canopy-app environment:
+
+
+```
+    conda activate canopy-app
+```
+
+- Run python script
+
+```
+python3 global_data_process.py
+```
diff --git a/python/environment.yml b/python/environment.yml
index c8421258..0a80ee97 100644
--- a/python/environment.yml
+++ b/python/environment.yml
@@ -21,3 +21,5 @@ dependencies:
   #
   # Extra
   - ipython
+  - pysolar
+  - scipy
diff --git a/python/global_data_process.py b/python/global_data_process.py
new file mode 100755
index 00000000..221cbac1
--- /dev/null
+++ b/python/global_data_process.py
@@ -0,0 +1,431 @@
+"""
+Created on Sun Jun 4 15:45:29 2023
+
+Author: Wei-Ting Hung
+"""
+
+import os
+import subprocess
+from datetime import datetime, timezone
+
+import numpy as np
+from netCDF4 import Dataset
+from pysolar.solar import get_altitude
+from scipy.interpolate import griddata
+
+"""User Options"""
+path = "/scratch/pcampbe8/canopy-app/input"  # work directory
+year = 2022  # year
+month = 7  # month
+day = 1  # day
+houri = 12  # gfs initialization hour in UTC (caution: currently GFS input files are initialized at 12 UTC only -- do not change)
+hour = 0  # gfs forecast hour (0-24) in UTC
+ref_lev = 10  # reference height (m, a.g.l.)
+frp_src = 1  # frp data source for WAF (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
+
+
+# ---------------------------------ATTENTION---------------------------------#
+# If local FRP is used (frp_src=0,1), archived GBBEPx files since 2020 are   #
+# available for GMU HOPPER users. For users outside GMU, parameter "f_frp"   #
+# and function "read_frp_local" need to be modified accordingly.             #
+# Function read_frp_local is designed for reading GBBEPx by default.         #
+#                                                                            #
+# Recent GBBEPx v3 files (~ < 3 months) are available for download at:       #
+# https://www.ospo.noaa.gov/Products/land/gbbepx/                            #
+# GBBEPx_all01GRID.emissions_v003_'+YY+MM+DD+'.nc'                           #
+#                                                                            #
+# Archived GBBEPx files since 2020 are available for GMU HOPPER users.       #
+#                                                                            #
+# 12 month climatological FRP will not be respective of actual conditions.   #
+# Only use it when users do not need the limited WAF application for fires.  #
+# ---------------------------------------------------------------------------#
+
+
+starttime = datetime.now()
+print("------------------------------------")
+print("---- Global input pre-process start!", starttime.strftime("%Y/%m/%d %H:%M:%S"))
+print("------------------------------------")
+
+
+"""Settings"""
+# date/time
+YY = str(year)
+MM = "%02d" % month
+DD = "%02d" % day
+HHI = "%02d" % houri
+HH = "%02d" % hour
+
+
+# domain
+lat_lim = [-90, 90]
+lon_lim = [0, 360]
+
+
+# input/output files
+f_met = (
+    path + "/gfs.t" + HHI + "z." + YY + MM + DD + ".sfcf0" + HH + ".nc"
+)  # gfs met file
+f_can = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + "01.sfcf000.nc"  # canopy file
+f_output = (
+    path + "/gfs.canopy.t" + HHI + "z." + YY + MM + DD + ".global.f0" + HH + ".nc"
+)  # output file
+
+if (frp_src == 0) or (frp_src == 1):  # local frp file
+    if int(YY + MM + DD) <= 20230510:  # version 3
+        f_frp = (
+            "/groups/ESS/yli74/data/GBBEPx/ORI/GBBEPx_all01GRID.emissions_v003_"
+            + YY
+            + MM
+            + DD
+            + ".nc"
+        )
+    else:  # version 4
+        f_frp = (
+            "/groups/ESS/yli74/data/GBBEPx/ORI/GBBEPx-all01GRID_v4r0_blend_"
+            + YY
+            + MM
+            + DD
+            + ".nc "
+        )
+elif frp_src == 2:  # climatological frp
+    f_frp = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + "01.sfcf000.nc"
+
+
+# required variables
+loclist = ["grid_xt", "lon", "grid_yt", "lat", "time"]
+metlist = [
+    "ugrd10m",
+    "vgrd10m",
+    "fricv",
+    "sfcr",
+    "vtype",
+    "sotyp",
+    "pressfc",
+    "dswrf",
+    "shtfl",
+    "tmpsfc",
+    "tmp2m",
+    "spfh2m",
+    "hpbl",
+    "prate_ave",
+]
+canlist = ["lai", "clu", "ffrac", "fh", "mol", "csz", "frp", "href"]
+
+
+# constants
+fill_value = 9.99e20  # fill value
+den = 1.18  # air density (kg/m3)
+Cp = 1004  # specific heat capacity of Air at 25C (J/kg/K)
+K = 0.4  # Von Karman constant
+g = 9.8  # gravitational acceleration (m/s2)
+
+
+# functions
+def read_varatt(var):
+    attname = var.ncattrs()
+    att = [var.getncattr(X) for X in attname]
+    return attname, att
+
+
+def write_varatt(var, attname, att):
+    for X in np.arange(len(attname)):
+        if attname[X] == "_FillValue":
+            continue
+        elif attname[X] == "missing_value":
+            value = np.float32(att[X])
+            value = np.round(value / 1e15) * 1e15
+            var.setncattr(attname[X], value)
+        else:
+            var.setncattr(attname[X], att[X])
+
+
+def mapping(xgrid, ygrid, data, xdata, ydata, map_method, fvalue):
+    output = griddata(
+        (xdata, ydata), data, (xgrid, ygrid), method=map_method, fill_value=fvalue
+    )
+    return output
+
+
+def read_gfs_climatology(filename, lat, lon, varname):
+    readin = Dataset(filename)
+
+    # map to met grids
+    yt = readin["lat"][:]
+    xt = readin["lon"][:]
+    data = np.squeeze(readin[varname][0, :, :])
+
+    DATA = mapping(lat, lon, data.flatten(), yt.flatten(), xt.flatten(), "linear", np.nan)
+    DATA[np.isnan(DATA)] = 0
+    DATA[DATA < 0] = 0
+    return DATA
+
+
+def read_frp_local(filename, lat, lon, fill_value):
+    readin = Dataset(filename)
+
+    # map to met grids
+    xt, yt = np.meshgrid(readin["Longitude"][:], readin["Latitude"][:])
+    xt[xt < 0] = xt[xt < 0] + 360
+    data = np.squeeze(readin["MeanFRP"][:])
+
+    DATA = mapping(
+        lat, lon, data.flatten(), yt.flatten(), xt.flatten(), "nearest", fill_value
+    )
+    return DATA
+
+
+"""Data Download"""
+"""Download from servers if required files do not exist."""
+print("---- Checking required files...")
+print("------------------------------------")
+
+# met file
+if os.path.isfile(f_met) is True:
+    print("---- Met file found!")
+else:
+    print("---- Cannot find met file. Downloading from AWS...")
+    subprocess.run(
+        [
+            "wget",
+            "--no-check-certificate",
+            "--no-proxy",
+            "-O",
+            path + "/gfs.t" + HHI + "z." + YY + MM + DD + ".sfcf0" + HH + ".nc",
+            "https://nacc-in-the-cloud.s3.amazonaws.com/inputs/"
+            + YY
+            + MM
+            + DD
+            + "/gfs.t"
+            + HHI
+            + "z.sfcf0"
+            + HH
+            + ".nc",
+        ]
+    )
+    if os.path.isfile(f_met) is True:
+        os.chmod(f_met, 0o0755)
+        print("---- Download complete!")
+    else:
+        print("---- No available met data. Terminated!")
+        exit()
+
+# can file
+if os.path.isfile(f_can) is True:
+    print("---- Canopy file found!")
+else:
+    print("---- Cannot find canopy file. Downloading from AWS...")
+    subprocess.run(
+        [
+            "wget",
+            "--no-check-certificate",
+            "--no-proxy",
+            "-P",
+            path,
+            "https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t"
+            + HHI
+            + "z."
+            + YY
+            + MM
+            + "01.sfcf000.nc",
+        ]
+    )
+    if os.path.isfile(f_can) is True:
+        os.chmod(f_can, 0o0755)
+        print("---- Download complete!")
+    else:
+        print("---- No available canopy data. Terminated!")
+        exit()
+
+# frp file
+if frp_src == 0:  # local source
+    if os.path.isfile(f_frp) is True:
+        os.system("cp " + f_frp + " " + path)
+        if int(YY + MM + DD) <= 20230510:
+            f_frp = path + "/GBBEPx_all01GRID.emissions_v003_" + YY + MM + DD + ".nc"
+        else:
+            f_frp = path + "/GBBEPx-all01GRID_v4r0_blend_" + YY + MM + DD + ".nc"
+        os.chmod(f_frp, 0o0755)
+        print("---- FRP file found!")
+    else:
+        print("---- No available FRP file. Terminated!")
+        exit()
+
+if frp_src == 1:  # local source
+    if os.path.isfile(f_frp) is True:
+        os.system("cp " + f_frp + " " + path)
+        if int(YY + MM + DD) <= 20230510:
+            f_frp = path + "/GBBEPx_all01GRID.emissions_v003_" + YY + MM + DD + ".nc"
+        else:
+            f_frp = path + "/GBBEPx-all01GRID_v4r0_blend_" + YY + MM + DD + ".nc"
+        os.chmod(f_frp, 0o0755)
+        print("---- FRP file found!")
+    else:
+        print("---- No available FRP file. Switch to Climatology FRP...")
+        frp_src = 2
+        f_frp = path + "/gfs.canopy.t" + HHI + "z." + YY + MM + "01.sfcf000.nc"
+
+if frp_src == 2:  # 12 month climatology frp
+    if os.path.isfile(f_frp) is True:
+        print("---- FRP file found!")
+    else:
+        print("---- Canot find FRP file. Downloading from AWS...")
+        subprocess.run(
+            [
+                "wget",
+                "--no-check-certificate",
+                "--no-proxy",
+                "-P",
+                path,
+                "https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t"
+                + HHI
+                + "z."
+                + YY
+                + MM
+                + "01.sfcf000.nc",
+            ]
+        )
+        if os.path.isfile(f_met) is True:
+            os.chmod(f_frp, 0o0755)
+            print("---- Download complete!")
+        else:
+            print("---- No available FRP data. Terminated!")
+            exit()
+
+    print("-----------!!!WARNING!!!-------------")
+    print("---!!!Climatological FRP is used!!!--")
+
+
+os.system("cp " + f_met + " " + f_output)  # copy gfs met file for appending
+
+
+"""Reading dimensions"""
+print("------------------------------------")
+print("---- Checking variable dimensions...")
+print("------------------------------------")
+readin = Dataset(f_met)
+grid_yt = readin["grid_yt"][:]
+grid_xt = readin["grid_xt"][:]
+lat = readin["lat"][:]
+lon = readin["lon"][:]
+time = readin["time"][:]
+
+
+# dimension sizes
+ntime = len(time)
+nlat = len(grid_yt)
+nlon = len(grid_xt)
+
+
+# var check
+print("time", time.shape)
+print("grid_yt", grid_yt.shape)
+print("grid_xt", grid_xt.shape)
+print("lat", lat.shape)
+print("lon", lon.shape)
+
+
+"""Adding canvar"""
+print("------------------------------------")
+print("---- Generating canopy variables...")
+print("------------------------------------")
+
+for i in np.arange(len(canlist)):
+    varname = canlist[i]
+
+    print("---- " + varname + " processing...")
+
+    if varname == "lai":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Leaf area index", "m^2/m^2", fill_value]
+        DATA = read_gfs_climatology(f_can, lat, lon, "lai")
+
+    elif varname == "clu":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Canopy clumping index", "none", fill_value]
+        DATA = read_gfs_climatology(f_can, lat, lon, "clu")
+
+    elif varname == "ffrac":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Forest fraction of grid cell", "none", fill_value]
+        DATA = read_gfs_climatology(f_can, lat, lon, "ffrac")
+
+    elif varname == "fh":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Canopy height above the surface", "m", fill_value]
+        DATA = read_gfs_climatology(f_can, lat, lon, "fh")
+
+    elif varname == "mol":
+        # Reference:
+        # Essa 1999, ESTIMATION OF MONIN-OBUKHOV LENGTH USING RICHARDSON AND BULK RICHARDSON NUMBER
+        # https://inis.iaea.org/collection/NCLCollectionStore/_Public/37/118/37118528.pdf
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Monin-Obukhov length", "m", fill_value]
+
+        readin = Dataset(f_met)
+        t2m = np.squeeze(readin["tmp2m"][:])
+        fricv = np.squeeze(readin["fricv"][:])
+        shtfl = np.squeeze(readin["shtfl"][:])
+
+        DATA = (-1 * den * Cp * t2m * (fricv**3)) / (K * g * shtfl)
+        DATA[DATA > 500] = 500
+        DATA[DATA < -500] = -500
+
+        del [readin, t2m, fricv, shtfl]
+
+    elif varname == "csz":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Cosine of solar zenith angle", "none", fill_value]
+
+        time_conv = datetime(
+            int(YY), int(MM), int(DD), int(HH), 0, 0, 0, tzinfo=timezone.utc
+        )
+        sza = 90 - get_altitude(lat, lon, time_conv)
+        DATA = np.cos(sza * 0.0174532925)  # degree to radian
+
+        del [time_conv, sza]
+
+    elif varname == "frp":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Mean fire radiative power", "MW", fill_value]
+
+        if frp_src == 2:
+            DATA = read_gfs_climatology(f_can, "frp")
+        else:
+            DATA = read_frp_local(f_frp, lat, lon, fill_value)
+
+    elif varname == "href":
+        ATTNAME = ["long_name", "units", "missing_value"]
+        ATT = ["Reference height above the surface", "m", fill_value]
+        DATA = np.empty([nlat, nlon])
+        DATA[:] = ref_lev
+
+    # var check
+    print("Dimension/Attributes:")
+    print(DATA.shape)
+    print(ATTNAME)
+    print(ATT)
+
+    # adding to output file
+    output = Dataset(f_output, "a")
+
+    var = output.createVariable(
+        varname, "float", ("time", "grid_yt", "grid_xt"), fill_value=fill_value
+    )
+    write_varatt(var, ATTNAME, ATT)
+    var[:] = DATA
+
+    output.close()
+
+    print("---- " + varname + " complete!")
+
+    del [output, var]
+    del [varname, DATA, ATTNAME, ATT]
+
+
+endtime = datetime.now()
+
+
+print("------------------------------------")
+print("---- Global input pre-process complete!", endtime.strftime("%Y/%m/%d %H:%M:%S"))
+print("---- Process time:", str(endtime - starttime))
+print("------------------------------------")

From 20e23b3e53d32600b60063b63b3d7b60e266e0d5 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 6 Jun 2023 11:48:16 -0400
Subject: [PATCH 20/64] Updated README.

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 7ecefac3..d1d8e6db 100644
--- a/README.md
+++ b/README.md
@@ -168,6 +168,9 @@ Hourly gridded GFSv16 data is available on AWS from March 23, 2021 - Current Day
 https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022MM01.sfcf000.nc
 ```
 
+You can also [generate global inputs using Python (see python/global_data_process.py script)](./python/README.md).
+
+
 ### Table 3. Current User Namelist Options
 
 | Namelist Option | Namelist Description and Units                                                     |

From 683e7c9c630f178fcbb39a398c1e1aa9bd6c2093 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 6 Jun 2023 11:50:13 -0400
Subject: [PATCH 21/64] Updated README.

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

diff --git a/README.md b/README.md
index d1d8e6db..f5d0ab38 100644
--- a/README.md
+++ b/README.md
@@ -168,7 +168,7 @@ Hourly gridded GFSv16 data is available on AWS from March 23, 2021 - Current Day
 https://nacc-in-the-cloud.s3.amazonaws.com/inputs/geo-files/gfs.canopy.t12z.2022MM01.sfcf000.nc
 ```
 
-You can also [generate global inputs using Python (see python/global_data_process.py script)](./python/README.md).
+You can also [generate global inputs using Python (see python/global_data_process.py)](./python/README.md).
 
 
 ### Table 3. Current User Namelist Options

From bc97f7456a4122500b1b07a3fc9bdd92981b8aca Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 6 Jun 2023 17:51:13 -0400
Subject: [PATCH 22/64] Initial commit to restructure tleaf and ppfd modules.

---
 src/Makefile               |   4 +-
 src/canopy_alloc.F90       |   8 ++-
 src/canopy_calcs.F90       |  24 +++++--
 src/canopy_canvars_mod.F90 |   4 ++
 src/canopy_dealloc.F90     |  14 +++--
 src/canopy_init.F90        |   8 ++-
 src/canopy_ppfd_mod.F90    | 126 +++++++++++++++++++++++++++++++++++++
 src/canopy_tleaf_mod.F90   | 122 +++++++++++++++++++++++++++++++++++
 8 files changed, 296 insertions(+), 14 deletions(-)
 create mode 100644 src/canopy_ppfd_mod.F90
 create mode 100644 src/canopy_tleaf_mod.F90

diff --git a/src/Makefile b/src/Makefile
index eeca9da2..b59b006f 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -63,9 +63,11 @@ OBJS :=\
  canopy_read_txt.o \
  canopy_dxcalc_mod.o \
  canopy_profile_mod.o \
+ canopy_phot_mod.o \
+ canopy_ppfd_mod.o \
+ canopy_tleaf_mod.o \
  canopy_wind_mod.o \
  canopy_waf_mod.o \
- canopy_phot_mod.o \
  canopy_eddy_mod.o \
  canopy_bioparm_mod.o \
  canopy_bioemi_mod.o \
diff --git a/src/canopy_alloc.F90 b/src/canopy_alloc.F90
index 46afb75a..ba007672 100644
--- a/src/canopy_alloc.F90
+++ b/src/canopy_alloc.F90
@@ -25,8 +25,12 @@ SUBROUTINE canopy_alloc
 ! Allocate arrays for Internal Canopy Distribution Variables
 !-------------------------------------------------------------------------------
 
-    if(.not.allocated(zhc))        allocate(zhc(modlays))
-    if(.not.allocated(fafraczInt)) allocate(fafraczInt(modlays))
+    if(.not.allocated(zhc))         allocate(zhc(modlays))
+    if(.not.allocated(fafraczInt))  allocate(fafraczInt(modlays))
+    if(.not.allocated(tleaf_sun))   allocate(tleaf_sun(modlays))
+    if(.not.allocated(tleaf_shade)) allocate(tleaf_shade(modlays))
+    if(.not.allocated(ppfd_sun))    allocate(ppfd_sun(modlays))
+    if(.not.allocated(ppfd_shade))  allocate(ppfd_shade(modlays))
 
 !-------------------------------------------------------------------------------
 ! Allocate arrays for Canopy Wind Outputs
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 3f47929b..eff0f621 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -15,11 +15,13 @@ SUBROUTINE canopy_calcs
     use canopy_utils_mod      !main canopy utilities
     use canopy_dxcalc_mod     !main canopy dx calculation
     use canopy_profile_mod    !main canopy foliage profile routines
+    use canopy_phot_mod       !main canopy radiation/photolysis attenuation components
+    use canopy_tleaf_mod      !main canopy leaf temperature components
+    use canopy_ppfd_mod       !main canopy leaf ppfd components
     use canopy_wind_mod       !main canopy wind components
-    use canopy_waf_mod
-    use canopy_phot_mod
-    use canopy_eddy_mod
-    use canopy_bioemi_mod
+    use canopy_waf_mod        !main canopy WAF components
+    use canopy_eddy_mod       !main canopy eddy diffusivity components
+    use canopy_bioemi_mod     !main canopy biogenic emissions components
 
     IMPLICIT NONE
 
@@ -150,6 +152,13 @@ SUBROUTINE canopy_calcs
                             if (ifcanbio) then
                                 if (cszref .ge. 0.0_rk .and. dswrfref .gt. 0.0_rk &
                                     .and. cluref .gt. 0.0_rk) then
+                                    !calculate sunlit/shade leaves, tleaf, and ppfd
+                                    call canopy_phot(fafraczInt, &
+                                        lairef, cluref, cszref, rjcf_3d(i,j,:))
+                                    call canopy_tleaf_lin( zk, hcmref, tmp2mref, tleaf_sun, tleaf_shade)
+                                    call canopy_ppfd_exp( zk, hcmref, dswrfref, lairef, ppfd_sun, &
+                                        ppfd_shade)
+                                    !calculate biogenic emissions
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
@@ -362,6 +371,13 @@ SUBROUTINE canopy_calcs
                         if (ifcanbio) then
                             if (cszref .ge. 0.0_rk .and. dswrfref .gt. 0.0_rk &
                                 .and. cluref .gt. 0.0_rk) then
+                                !calculate sunlit/shade leaves, tleaf, and ppfd
+                                call canopy_phot(fafraczInt, &
+                                    lairef, cluref, cszref, rjcf(loc, :))
+                                call canopy_tleaf_lin( zk, hcmref, tmp2mref, tleaf_sun, tleaf_shade)
+                                call canopy_ppfd_exp( zk, hcmref, dswrfref, lairef, ppfd_sun, &
+                                    ppfd_shade)
+                                !calculate biogenic emissions
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &
diff --git a/src/canopy_canvars_mod.F90 b/src/canopy_canvars_mod.F90
index 9365262c..1c5ff989 100644
--- a/src/canopy_canvars_mod.F90
+++ b/src/canopy_canvars_mod.F90
@@ -33,6 +33,10 @@ MODULE canopy_canvars_mod
     real(rk), allocatable :: fainc         ( : )          ! incremental foliage shape function
     real(rk), allocatable :: fafracz       ( : )          ! incremental fractional foliage shape function
     real(rk), allocatable :: fafraczInt    ( : )          ! integral of incremental fractional foliage shape function
+    real(rk), allocatable :: tleaf_sun     ( : )          ! Leaf temp for sunlit leaves (K)
+    real(rk), allocatable :: tleaf_shade   ( : )          ! Leaf temp for shaded leaves (K)
+    real(rk), allocatable :: ppfd_sun      ( : )          ! PPFD for sunlit leaves (umol phot/m2 s)
+    real(rk), allocatable :: ppfd_shade    ( : )          ! PPFD for shaded leaves (umol phot/m2 s)
     real(rk), allocatable :: canBOT        ( : )          ! Canopy bottom wind reduction factors
     real(rk), allocatable :: canTOP        ( : )          ! Canopy top wind reduction factors
     real(rk), allocatable :: canWIND       ( : , : )      ! canopy wind speeds (m/s)
diff --git a/src/canopy_dealloc.F90 b/src/canopy_dealloc.F90
index 2094a096..6a65359b 100644
--- a/src/canopy_dealloc.F90
+++ b/src/canopy_dealloc.F90
@@ -25,11 +25,15 @@ SUBROUTINE canopy_dealloc
 ! Dellocate arrays for Canopy Distribution
 !-------------------------------------------------------------------------------
 
-    if(allocated(zk))         deallocate(zk) !allocated in canopy_readnml
-    if(allocated(zhc))        deallocate(zhc)
-    if(allocated(fainc))      deallocate(fainc) !allocated in canopy_profile
-    if(allocated(fafracz))    deallocate(fafracz) !allocated in canopy_profile
-    if(allocated(fafraczInt)) deallocate(fafraczInt)
+    if(allocated(zk))          deallocate(zk) !allocated in canopy_readnml
+    if(allocated(zhc))         deallocate(zhc)
+    if(allocated(fainc))       deallocate(fainc) !allocated in canopy_profile
+    if(allocated(fafracz))     deallocate(fafracz) !allocated in canopy_profile
+    if(allocated(fafraczInt))  deallocate(fafraczInt)
+    if(allocated(tleaf_sun))   deallocate(tleaf_sun)
+    if(allocated(tleaf_shade)) deallocate(tleaf_shade)
+    if(allocated(ppfd_sun))    deallocate(ppfd_sun)
+    if(allocated(ppfd_shade))  deallocate(ppfd_shade)
 
 !-------------------------------------------------------------------------------
 ! Deallocate arrays for Canopy Wind
diff --git a/src/canopy_init.F90 b/src/canopy_init.F90
index d7af1183..bda4345f 100644
--- a/src/canopy_init.F90
+++ b/src/canopy_init.F90
@@ -19,8 +19,12 @@ SUBROUTINE canopy_init
 ! Initialize arrays for Canopy Distribution
 !-------------------------------------------------------------------------------
 
-    if(allocated(zhc))        zhc(:)        = fillreal
-    if(allocated(fafraczInt)) fafraczInt(:) = fillreal
+    if(allocated(zhc))          zhc(:)         = fillreal
+    if(allocated(fafraczInt))   fafraczInt(:)  = fillreal
+    if(allocated(tleaf_sun))    tleaf_sun(:)   = fillreal
+    if(allocated(tleaf_shade))  tleaf_shade(:) = fillreal
+    if(allocated(ppfd_sun))     ppfd_sun(:)    = fillreal
+    if(allocated(ppfd_shade))   ppfd_shade(:)  = fillreal
 
 !-------------------------------------------------------------------------------
 ! Initialize arrays for Canopy Wind
diff --git a/src/canopy_ppfd_mod.F90 b/src/canopy_ppfd_mod.F90
new file mode 100644
index 00000000..0a270bda
--- /dev/null
+++ b/src/canopy_ppfd_mod.F90
@@ -0,0 +1,126 @@
+module canopy_ppfd_mod
+
+    implicit none
+
+contains
+
+!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+    SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
+
+!-----------------------------------------------------------------------
+
+! Description:
+!     computes linear interpolation method for tleaf sun/shade in canopy.
+
+! Preconditions:
+!     in-canopy height, and model LAI, clumping index, and solar zenith angle
+
+! Subroutines and Functions Called:
+
+! Revision History:
+!     Prototype 06/23 by PCC
+!     Jun 2023 P.C. Campbell: Initial standalone tleaf linear subroutine based on
+!                             Silva et al. (2020) algorithms
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+        use canopy_const_mod, ONLY: RK     !constants for canopy models
+        use canopy_utils_mod,  ONLY: interp_linear1_internal
+
+! Arguments:
+!     IN/OUT
+        REAL(RK),    INTENT( IN )       :: ZK(:)                          ! Input model heights (m)
+        REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
+        REAL(RK),    INTENT( IN )       :: SFCRAD                         ! Model input Instantaneous surface downward shortwave flux (W/m2)
+        REAL(RK),    INTENT( IN )       :: LAI                            ! Model input total Leaf Area Index
+        REAL(RK),    INTENT( OUT )      :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( OUT )      :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
+
+!      LOCAL
+        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
+        !top of canopy
+        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
+        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
+        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
+        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
+        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
+
+        REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
+
+        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
+        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
+        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
+        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
+
+        integer i
+
+! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
+! through canopy
+!Citation:
+!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
+!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
+!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
+        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
+            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
+                CTEMP_SUN(i)   = 0.0
+                DTEMP_SUN(i)   = 0.0
+                CTEMP_SHADE(i) = 0.0
+                DTEMP_SHADE(i) = 0.0
+            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
+            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
+            end if
+        end do
+
+        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
+        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
+
+    END SUBROUTINE CANOPY_PPFD_EXP
+
+end module canopy_ppfd_mod
diff --git a/src/canopy_tleaf_mod.F90 b/src/canopy_tleaf_mod.F90
new file mode 100644
index 00000000..a5c172dd
--- /dev/null
+++ b/src/canopy_tleaf_mod.F90
@@ -0,0 +1,122 @@
+module canopy_tleaf_mod
+
+    implicit none
+
+contains
+
+!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+    SUBROUTINE CANOPY_TLEAF_LIN( ZK, FCH, TEMP2, TLEAF_SUN, TLEAF_SHADE)
+
+!-----------------------------------------------------------------------
+
+! Description:
+!     computes linear interpolation method for tleaf sun/shade in canopy.
+
+! Preconditions:
+!     canopy height,in-canopy model height, 2-m temp
+
+! Subroutines and Functions Called:
+
+! Revision History:
+!     Prototype 06/23 by PCC
+!     Jun 2023 P.C. Campbell: Initial standalone tleaf linear subroutine based on
+!                             Silva et al. (2020) algorithms
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+        use canopy_const_mod, ONLY: RK     !constants for canopy models
+        use canopy_utils_mod,  ONLY: interp_linear1_internal
+
+! Arguments:
+!     IN/OUT
+        REAL(RK),    INTENT( IN )       :: ZK(:)                          ! Input model heights (m)
+        REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
+        REAL(RK),    INTENT( IN )       :: TEMP2                          ! Model input 2-m Temperature (K
+        REAL(RK),    INTENT( OUT )      :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
+        REAL(RK),    INTENT( OUT )      :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
+
+!      LOCAL
+        !Linearized 2-m temp --> leaf temp parameters Based on Table 1 in Silva et al. (2020)
+        REAL(RK),          PARAMETER     :: ATEMP_1_SUN     =  -13.891_rk !Level 1 = top of canopy
+        REAL(RK),          PARAMETER     :: ATEMP_2_SUN     =  -12.322_rk !...
+        REAL(RK),          PARAMETER     :: ATEMP_3_SUN     =  -1.032_rk  !...
+        REAL(RK),          PARAMETER     :: ATEMP_4_SUN     =  -5.172_rk  !...
+        REAL(RK),          PARAMETER     :: ATEMP_5_SUN     =  -5.589_rk  !...
+        REAL(RK),          PARAMETER     :: BTEMP_1_SUN     =  1.064_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_2_SUN     =  1.057_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_3_SUN     =  1.031_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_4_SUN     =  1.050_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_5_SUN     =  1.051_rk   !...
+        REAL(RK),          PARAMETER     :: ATEMP_1_SHADE   =  -12.846_rk !...
+        REAL(RK),          PARAMETER     :: ATEMP_2_SHADE   =  -11.343_rk !...
+        REAL(RK),          PARAMETER     :: ATEMP_3_SHADE   =  -1.068_rk  !...
+        REAL(RK),          PARAMETER     :: ATEMP_4_SHADE   =  -5.551_rk  !...
+        REAL(RK),          PARAMETER     :: ATEMP_5_SHADE   =  -5.955_rk  !...
+        REAL(RK),          PARAMETER     :: BTEMP_1_SHADE   =  1.060_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_2_SHADE   =  1.053_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_3_SHADE   =  1.031_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_4_SHADE   =  1.051_rk   !...
+        REAL(RK),          PARAMETER     :: BTEMP_5_SHADE   =  1.053_rk   !...
+        REAL(RK) :: ATEMP_SUN(SIZE(ZK))            ! Regression coefficient A for sun leaves (Silva et al., 2020)
+        REAL(RK) :: BTEMP_SUN(SIZE(ZK))            ! Regression coefficient B for sun leaves
+        REAL(RK) :: ATEMP_SHADE(SIZE(ZK))          ! Regression coefficient A for shade leaves
+        REAL(RK) :: BTEMP_SHADE(SIZE(ZK))          ! Regression coefficient B for shade leaves
+
+        integer i
+
+! Use linear canopy temperature model based on Silva et al. (2020) to get approx. sun/shade leaf temperatures
+! through canopy (ignores effect of wind speed on leaf boundary layer ~ 1 % error/bias)
+!Citation:
+!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
+!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
+!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
+        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
+            if (ZK(i) .gt. FCH) then ! above canopy, Tleaf = Tair
+                ATEMP_SUN(i)   = 0.0
+                BTEMP_SUN(i)   = 1.0
+                ATEMP_SHADE(i) = 0.0
+                BTEMP_SHADE(i) = 1.0
+            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ ATEMP_2_SUN,ATEMP_1_SUN /),ZK(i))
+                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ BTEMP_2_SUN,BTEMP_1_SUN /),ZK(i))
+                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ ATEMP_2_SHADE,ATEMP_1_SHADE /),ZK(i))
+                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ BTEMP_2_SHADE,BTEMP_1_SHADE /),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
+                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ ATEMP_3_SUN,ATEMP_2_SUN /),ZK(i))
+                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ BTEMP_3_SUN,BTEMP_2_SUN /),ZK(i))
+                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ ATEMP_3_SHADE,ATEMP_2_SHADE /),ZK(i))
+                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ BTEMP_3_SHADE,BTEMP_2_SHADE /),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
+                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ ATEMP_4_SUN,ATEMP_3_SUN /),ZK(i))
+                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ BTEMP_4_SUN,BTEMP_3_SUN /),ZK(i))
+                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ ATEMP_4_SHADE,ATEMP_3_SHADE /),ZK(i))
+                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ BTEMP_4_SHADE,BTEMP_3_SHADE /),ZK(i))
+            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+                ATEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ ATEMP_5_SUN,ATEMP_4_SUN /),ZK(i))
+                BTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ BTEMP_5_SUN,BTEMP_4_SUN /),ZK(i))
+                ATEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ ATEMP_5_SHADE,ATEMP_4_SHADE /),ZK(i))
+                BTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ BTEMP_5_SHADE,BTEMP_4_SHADE /),ZK(i))
+            end if
+        end do
+
+        TLEAF_SUN   = ATEMP_SUN + (BTEMP_SUN*TEMP2)
+        TLEAF_SHADE = ATEMP_SHADE + (BTEMP_SHADE*TEMP2)
+
+    END SUBROUTINE CANOPY_TLEAF_LIN
+
+end module canopy_tleaf_mod

From 82516878bd15f3fb9a9f8c612dc823ae9b9017d6 Mon Sep 17 00:00:00 2001
From: zmoon <zmoon92@gmail.com>
Date: Tue, 6 Jun 2023 16:13:36 -0600
Subject: [PATCH 23/64] Attempt to clarify HREF meaning in code comments

---
 src/canopy_profile_mod.F90 | 4 ++--
 src/canopy_wind_mod.F90    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/canopy_profile_mod.F90 b/src/canopy_profile_mod.F90
index 5882a5a6..ee5506bd 100644
--- a/src/canopy_profile_mod.F90
+++ b/src/canopy_profile_mod.F90
@@ -245,13 +245,13 @@ SUBROUTINE CANOPY_ZPD( ZHC, FCLAI, UBZREF, Z0GHC, &
         REAL(RK),    INTENT( IN )  :: ZHC     ( : )   ! SUB-CANOPY Total z/h layers (nondimensional)
         REAL(RK),    INTENT( IN )  :: FCLAI   ( : )   ! SUB-CANOPY Fractional (z) shapes of the
         ! plant surface distribution, i.e., a Fractional Culmulative LAI
-        REAL(RK),    INTENT( IN )  :: UBZREF          ! Mean wind speed at zref-height of canopy top (m/s)
+        REAL(RK),    INTENT( IN )  :: UBZREF          ! Mean wind speed at reference height (ZREF) (m/s)
         REAL(RK),    INTENT( IN )  :: Z0GHC           ! Ratio of ground roughness length to canopy top height (nondimensional)
         REAL(RK),    INTENT( IN )  :: LAMBDARS         ! Value representing influence of roughness sublayer (nondimensional)
         REAL(RK),    INTENT( IN )  :: CDRAG           ! Drag coefficient (nondimensional)
         REAL(RK),    INTENT( IN )  :: PAI             ! Total plant/foliage area index (nondimensional)
         REAL(RK),    INTENT( IN )  :: FCH             ! Grid cell canopy height (m)
-        REAL(RK),    INTENT( IN )  :: HREF            ! Reference Height (m) above the canopy
+        REAL(RK),    INTENT( IN )  :: HREF            ! Reference Height above the canopy (ZREF = FCH + HREF; m)
         REAL(RK),    INTENT( IN )  :: Z0_MOD          ! Input model value of surface roughness length, z0 (m)
         INTEGER,     INTENT( IN )  :: VTYPE           ! Grid cell dominant vegetation type
         INTEGER,     INTENT( IN )  :: LU_OPT          ! integer for LU type from model mapped to Massman et al. (default = 0/VIIRS)
diff --git a/src/canopy_wind_mod.F90 b/src/canopy_wind_mod.F90
index 53f87d51..6b6e846e 100644
--- a/src/canopy_wind_mod.F90
+++ b/src/canopy_wind_mod.F90
@@ -33,12 +33,12 @@ SUBROUTINE CANOPY_WIND_MOST( HCM, ZK, FAFRACK, UBZREF, Z0GHC, &
         REAL(RK),    INTENT( IN )  :: ZK               ! Above/Below canopy height, z (m)
         REAL(RK),    INTENT( IN )  :: FAFRACK          ! Fractional (z) shapes of the
         ! plant surface distribution (nondimensional)
-        REAL(RK),    INTENT( IN )  :: UBZREF           ! Mean wind speed at reference height (m/s)
+        REAL(RK),    INTENT( IN )  :: UBZREF           ! Mean wind speed at reference height (ZREF) (m/s)
         REAL(RK),    INTENT( IN )  :: Z0GHC            ! Ratio of ground roughness length to canopy top height (nondimensional)
         REAL(RK),    INTENT( IN )  :: LAMBDARS         ! Value representing influence of roughness sublayer (nondimensional)
         REAL(RK),    INTENT( IN )  :: CDRAG            ! Drag coefficient (nondimensional)
         REAL(RK),    INTENT( IN )  :: PAI              ! Total plant/foliage area index (nondimensional)
-        REAL(RK),    INTENT( IN )  :: HREF             ! Reference Height above canopy associated with ref wind speed  (m)
+        REAL(RK),    INTENT( IN )  :: HREF             ! Reference Height above the canopy (ZREF = HCM + HREF; m)
         REAL(RK),    INTENT( IN )  :: D_H              ! Zero plane displacement heights (nondimensional)
         REAL(RK),    INTENT( IN )  :: ZO_H             ! Surface (soil+veg) roughness lengths (nondimensional)
         REAL(RK),    INTENT( OUT ) :: CANBOT_OUT       ! Canopy bottom wind reduction factor = canbot (nondimensional)

From 7326526c86e3e3b93d92d2660188e6e239b0099a Mon Sep 17 00:00:00 2001
From: zmoon <zmoon92@gmail.com>
Date: Tue, 6 Jun 2023 16:19:39 -0600
Subject: [PATCH 24/64] More href edits

---
 README.md                     | 4 ++--
 python/README.md              | 2 +-
 python/global_data_process.py | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index f5d0ab38..86e2c6b2 100644
--- a/README.md
+++ b/README.md
@@ -146,7 +146,7 @@ The Canopy-App input data in [Table 2](#table-2-canopy-app-required-input-variab
 | `frp`                            | Total Fire Radiative Power (MW/grid cell area) | [NOAA/NESDIS GBBEPx](https://www.ospo.noaa.gov/Products/land/gbbepx/) |
 | `csz`                            | Cosine of the solar zenith angle (dimensionless) | [Based on Python Pysolar](https://pysolar.readthedocs.io/en/latest/) |
 | `mol`                            | Monin-Obukhov Length (m)                    | Externally calculated using GFS `tmp2m`, `fricv`, and `shtfl`.  ([Essa, 1999](https://inis.iaea.org/collection/NCLCollectionStore/_Public/37/118/37118528.pdf)) |
-| `href`                           | Reference height above canopy (m) - 10 m    | Added as a constant reference height above surface (i.e., 10 m).  Can be taken from NL. |
+| `href`                           | Reference height above canopy (m) - 10 m    | Assumed constant (i.e., 10 m).  Can be taken from NL. |
 
 **More Information on Data Sources from [Table 2](#table-2-canopy-app-required-input-variables):**
 
@@ -185,7 +185,7 @@ You can also [generate global inputs using Python (see python/global_data_proces
 | `ifcaneddy`     | logical canopy eddy Kz option (default: `.FALSE.`)                                 |
 | `ifcanphot`     | logical canopy photolysis option (default: `.FALSE.`)                              |
 | `ifcanbio`      | logical canopy biogenic emissions option (default: `.FALSE.`)                      |
-| `href_opt`      | integer for using href_set in namelist (= `0`, default) or array from file (= `1`) |
+| `href_opt`      | integer for using `href_set` in namelist (= `0`, default) or array from file (= `1`) |
 | `href_set`      | user-set real value of reference height above canopy associated with input wind speed (m) (only used if `href_opt=0`) **\*\*\*** |
 | `z0ghc`         | ratio of ground roughness length to canopy top height (Massman et al., 2017)       |
 | `rsl_opt`       | user-set option for either MOST or unified Roughness SubLayer (RSL) effects above and at canopy top (Uc).(= `0`, default: uses MOST and a constant lambdars factor only), (= `1`, under development: will use a more unified RSL approach from Bonan et al. (2018) and Abolafia-Rosenzweig et al., 2021)   |
diff --git a/python/README.md b/python/README.md
index 06faa58e..ed6e2114 100644
--- a/python/README.md
+++ b/python/README.md
@@ -70,7 +70,7 @@ month    = 7      # month
 day      = 1      # day
 houri    = 12     # gfs initialization hour in UTC (caution currently GFS files are initialized at 12 UTC only -- do not change)
 hour     = 00     # gfs forecast hour in UTC
-ref_lev  = 10     # reference height (m, a.g.l.)
+ref_lev  = 10     # reference height above the canopy (m)
 frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
 ```
 
diff --git a/python/global_data_process.py b/python/global_data_process.py
index 221cbac1..3bb33403 100755
--- a/python/global_data_process.py
+++ b/python/global_data_process.py
@@ -20,7 +20,7 @@
 day = 1  # day
 houri = 12  # gfs initialization hour in UTC (caution: currently GFS input files are initialized at 12 UTC only -- do not change)
 hour = 0  # gfs forecast hour (0-24) in UTC
-ref_lev = 10  # reference height (m, a.g.l.)
+ref_lev = 10  # reference height above the canopy (m)
 frp_src = 1  # frp data source for WAF (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
 
 
@@ -395,7 +395,7 @@ def read_frp_local(filename, lat, lon, fill_value):
 
     elif varname == "href":
         ATTNAME = ["long_name", "units", "missing_value"]
-        ATT = ["Reference height above the surface", "m", fill_value]
+        ATT = ["Reference height above the canopy", "m", fill_value]
         DATA = np.empty([nlat, nlon])
         DATA[:] = ref_lev
 

From 59d96700c05f9a1f14d0dc65738f0810dd3b2233 Mon Sep 17 00:00:00 2001
From: zmoon <zmoon92@gmail.com>
Date: Tue, 6 Jun 2023 16:22:49 -0600
Subject: [PATCH 25/64] md

---
 python/README.md | 49 +++++++++++++++++++++++-------------------------
 1 file changed, 23 insertions(+), 26 deletions(-)

diff --git a/python/README.md b/python/README.md
index ed6e2114..22a45080 100644
--- a/python/README.md
+++ b/python/README.md
@@ -52,37 +52,34 @@ ds = run_config_sens(cases)
 ```
 :point_up: We still get a single output dataset, but it has a `case` dimension.
 
-:point_down: You can also download and generate global gridded canopy-app inputs using python.
+### Generating global data
 
-- Edit python script (`global_data_process.py`)
+You can also download and generate global gridded canopy-app inputs using Python.
 
-```
-vim global_data_process.py
-```
-
-- Change user settings
+1. Edit python script (`global_data_process.py`)
 
-```
-'''User Options'''
-path     = '/scratch/pcampbe8/canopy-app/input'    # work directory
-year     = 2022   # year
-month    = 7      # month
-day      = 1      # day
-houri    = 12     # gfs initialization hour in UTC (caution currently GFS files are initialized at 12 UTC only -- do not change)
-hour     = 00     # gfs forecast hour in UTC
-ref_lev  = 10     # reference height above the canopy (m)
-frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
-```
+2. Change user settings
 
-- Activate Python canopy-app environment:
+   ```python
+   '''User Options'''
+   path     = '/scratch/pcampbe8/canopy-app/input'  # work directory
+   year     = 2022   # year
+   month    = 7      # month
+   day      = 1      # day
+   houri    = 12     # gfs initialization hour in UTC (caution currently GFS files are initialized at 12 UTC only -- do not change)
+   hour     = 00     # gfs forecast hour in UTC
+   ref_lev  = 10     # reference height above the canopy (m)
+   frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
+   ```
 
+2. Activate canopy-app Conda environment:
 
-```
-    conda activate canopy-app
-```
+   ```
+   conda activate canopy-app
+   ```
 
-- Run python script
+3. Run python script
 
-```
-python3 global_data_process.py
-```
+   ```
+   python global_data_process.py
+   ```

From ca03333fc6c36b41da5b86dc6f4484cce552fbe2 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Tue, 6 Jun 2023 21:10:41 -0400
Subject: [PATCH 26/64] Reverted changes to wait for bio_opts changes.

---
 src/canopy_calcs.F90 | 24 ++++--------------------
 1 file changed, 4 insertions(+), 20 deletions(-)

diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index eff0f621..3f47929b 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -15,13 +15,11 @@ SUBROUTINE canopy_calcs
     use canopy_utils_mod      !main canopy utilities
     use canopy_dxcalc_mod     !main canopy dx calculation
     use canopy_profile_mod    !main canopy foliage profile routines
-    use canopy_phot_mod       !main canopy radiation/photolysis attenuation components
-    use canopy_tleaf_mod      !main canopy leaf temperature components
-    use canopy_ppfd_mod       !main canopy leaf ppfd components
     use canopy_wind_mod       !main canopy wind components
-    use canopy_waf_mod        !main canopy WAF components
-    use canopy_eddy_mod       !main canopy eddy diffusivity components
-    use canopy_bioemi_mod     !main canopy biogenic emissions components
+    use canopy_waf_mod
+    use canopy_phot_mod
+    use canopy_eddy_mod
+    use canopy_bioemi_mod
 
     IMPLICIT NONE
 
@@ -152,13 +150,6 @@ SUBROUTINE canopy_calcs
                             if (ifcanbio) then
                                 if (cszref .ge. 0.0_rk .and. dswrfref .gt. 0.0_rk &
                                     .and. cluref .gt. 0.0_rk) then
-                                    !calculate sunlit/shade leaves, tleaf, and ppfd
-                                    call canopy_phot(fafraczInt, &
-                                        lairef, cluref, cszref, rjcf_3d(i,j,:))
-                                    call canopy_tleaf_lin( zk, hcmref, tmp2mref, tleaf_sun, tleaf_shade)
-                                    call canopy_ppfd_exp( zk, hcmref, dswrfref, lairef, ppfd_sun, &
-                                        ppfd_shade)
-                                    !calculate biogenic emissions
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
                                         lairef, cluref, cszref, dswrfref, tmp2mref, &
@@ -371,13 +362,6 @@ SUBROUTINE canopy_calcs
                         if (ifcanbio) then
                             if (cszref .ge. 0.0_rk .and. dswrfref .gt. 0.0_rk &
                                 .and. cluref .gt. 0.0_rk) then
-                                !calculate sunlit/shade leaves, tleaf, and ppfd
-                                call canopy_phot(fafraczInt, &
-                                    lairef, cluref, cszref, rjcf(loc, :))
-                                call canopy_tleaf_lin( zk, hcmref, tmp2mref, tleaf_sun, tleaf_shade)
-                                call canopy_ppfd_exp( zk, hcmref, dswrfref, lairef, ppfd_sun, &
-                                    ppfd_shade)
-                                !calculate biogenic emissions
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
                                     lairef, cluref, cszref, dswrfref, tmp2mref, &

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 27/64] 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 28/64] 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 49f0110c48f530119b7f7cc653d66607fd539349 Mon Sep 17 00:00:00 2001
From: quaz115 <quazi.rasool@noaa.gov>
Date: Thu, 8 Jun 2023 19:15:27 -0600
Subject: [PATCH 29/64] Modified Makefile to work with both ifort or gfortran
 to build canopy-app

---
 src/Makefile | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index eeca9da2..e934dd1d 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -2,10 +2,13 @@
 # Use `FC=<compiler> ... make` to select compiler
 # Use `DEBUG=1 ... make` for a debug build
 # Use `NETCDF=1 ... make` to build with NetCDF using `nf-config`
+# compile with either FC=ifort or FC=gfortran
 
 # Compiler
 FC ?= gfortran
 ifeq ($(FC), f77)  # override possible Make default
+  FC := ifort 
+else ifeq ($(FC),gfortran)
   FC := gfortran
 endif
 $(info FC setting: '$(FC)')
@@ -19,7 +22,12 @@ NETCDF ?= 1
 # Compile flags
 $(info DEBUG setting: '$(DEBUG)')
 ifeq ($(DEBUG), 1)
-  FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5
+  ifeq ($(FC),gfortran)
+    FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 
+  else ifeq ($(FC),ifort)
+    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags, builds with warnings on Hera
+    FCFLAGS  := -g -warn all -check bounds -traceback #builds without warnings on Hera
+  endif
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3
 else

From 55ba56dc6548974a1e9d8a3c80cd77ce3789c3b6 Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Thu, 8 Jun 2023 22:26:36 -0400
Subject: [PATCH 30/64] Update src/Makefile

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 src/Makefile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index e934dd1d..393deb85 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -2,7 +2,6 @@
 # Use `FC=<compiler> ... make` to select compiler
 # Use `DEBUG=1 ... make` for a debug build
 # Use `NETCDF=1 ... make` to build with NetCDF using `nf-config`
-# compile with either FC=ifort or FC=gfortran
 
 # Compiler
 FC ?= gfortran

From 91b5b43fd4502f0572497baf8104193bcf4fd177 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Thu, 8 Jun 2023 19:42:50 -0700
Subject: [PATCH 31/64] Update Makefile

---
 src/Makefile | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index 393deb85..6aa2e8b7 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -6,8 +6,6 @@
 # Compiler
 FC ?= gfortran
 ifeq ($(FC), f77)  # override possible Make default
-  FC := ifort 
-else ifeq ($(FC),gfortran)
   FC := gfortran
 endif
 $(info FC setting: '$(FC)')

From cb97f66ab3222223a342ff665aa11b955ad11160 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Thu, 8 Jun 2023 19:59:45 -0700
Subject: [PATCH 32/64] Update Makefile ifort

---
 src/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index 6aa2e8b7..933a1c23 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -6,7 +6,7 @@
 # Compiler
 FC ?= gfortran
 ifeq ($(FC), f77)  # override possible Make default
-  FC := gfortran
+  FC := ifort
 endif
 $(info FC setting: '$(FC)')
 

From 0798252e2c86b7119abdad40bb8c0e112f6f9445 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Thu, 8 Jun 2023 20:20:55 -0700
Subject: [PATCH 33/64] Update Makefile- Latest build check with ifort on Hera,
 both debug flag options work without warning

---
 src/Makefile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index 933a1c23..4e01faba 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -22,8 +22,9 @@ ifeq ($(DEBUG), 1)
   ifeq ($(FC),gfortran)
     FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 
   else ifeq ($(FC),ifort)
-    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags, builds with warnings on Hera
-    FCFLAGS  := -g -warn all -check bounds -traceback #builds without warnings on Hera
+    # Both the following Debug flag options build Canopy-app on Hera with ifort without warnings 
+    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags
+    FCFLAGS  := -g -warn all -check bounds -traceback 
   endif
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3

From fd24cb156906eb9d3ce996511a894d5052322864 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Thu, 8 Jun 2023 21:07:31 -0700
Subject: [PATCH 34/64] Update Makefile- Resolved, one debug flag (ifort) gives
 warning

---
 src/Makefile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index 4e01faba..254b839b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -6,7 +6,7 @@
 # Compiler
 FC ?= gfortran
 ifeq ($(FC), f77)  # override possible Make default
-  FC := ifort
+  FC := gfortran
 endif
 $(info FC setting: '$(FC)')
 
@@ -22,9 +22,9 @@ ifeq ($(DEBUG), 1)
   ifeq ($(FC),gfortran)
     FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 
   else ifeq ($(FC),ifort)
-    # Both the following Debug flag options build Canopy-app on Hera with ifort without warnings 
-    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags
-    FCFLAGS  := -g -warn all -check bounds -traceback 
+    # Tested the following Debug flag options on Hera with 'DEBUG=1 NETCDF=1 FC=ifort make -C src'
+    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags  #builds but with WARNINGS to be resolved 
+    FCFLAGS  := -g -warn all -check bounds -traceback  #builds Canopy-app on Hera with FC=ifort without warnings
   endif
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3

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 35/64] 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 36/64] 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 37/64] 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 b4bf7cf0c5b50469c10995ea9287ea2720797c59 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Fri, 9 Jun 2023 13:19:08 -0700
Subject: [PATCH 38/64] Update Makefile- $NETCDF to $NC (ifort builds and make
 clean without error/warning)

---
 src/Makefile | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index 254b839b..c2cacd2f 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,7 +1,7 @@
 #
 # Use `FC=<compiler> ... make` to select compiler
 # Use `DEBUG=1 ... make` for a debug build
-# Use `NETCDF=1 ... make` to build with NetCDF using `nf-config`
+# Use `NC=1 ... make` to build with NetCDF using `nf-config`
 
 # Compiler
 FC ?= gfortran
@@ -14,17 +14,18 @@ $(info FC setting: '$(FC)')
 DEBUG ?= 0
 
 # Default to NetCDF build
-NETCDF ?= 1
+NC ?= 1
 
 # Compile flags
 $(info DEBUG setting: '$(DEBUG)')
 ifeq ($(DEBUG), 1)
   ifeq ($(FC),gfortran)
-    FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 
+    FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 -std=f2003 -fall-intrinsics
   else ifeq ($(FC),ifort)
-    # Tested the following Debug flag options on Hera with 'DEBUG=1 NETCDF=1 FC=ifort make -C src'
-    #FCFLAGS := -g -warn all -implicitnone -O1 -stand f90 -error-limit 5  #Equivalent to gfortran Debug flags  #builds but with WARNINGS to be resolved 
-    FCFLAGS  := -g -warn all -check bounds -traceback  #builds Canopy-app on Hera with FC=ifort without warnings
+    # Tested the following Debug flag options on Hera with 'DEBUG=1 NC=1 FC=ifort make -C src'
+    # Both options build without warnings and also make clean in src
+    FCFLAGS := -g -warn all -implicitnone -O1 -error-limit 5  #Equivalent to gfortran Debug flags
+    #FCFLAGS  := -g -warn all -check bounds -traceback  #also builds Canopy-app on Hera with FC=ifort without warnings
   endif
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3
@@ -35,18 +36,18 @@ endif
 # NETCDF Settings here
 LIBS :=
 INC :=
-$(info NETCDF setting: '$(NETCDF)')
-ifeq ($(NETCDF), 1)
+$(info NETCDF setting: '$(NC)')
+ifeq ($(NC), 1)
   NETCDF_FLIBS := $(shell nf-config --flibs)
   NETCDF_INC := -I$(shell nf-config --includedir)
   #
   LIBS += $(NETCDF_FLIBS)
   INC += $(NETCDF_INC)
   FCFLAGS += -DNETCDF
-else ifeq ($(NETCDF), 0)
+else ifeq ($(NC), 0)
   #
 else
-  $(error invalid setting for NETCDF, should be 0 or 1 but is '$(NETCDF)')
+  $(error invalid setting for NETCDF, should be 0 or 1 but is '$(NC)')
 endif
 $(info LIBS: '$(LIBS)')
 $(info INC:  '$(INC)')
@@ -80,7 +81,7 @@ OBJS :=\
  canopy_dealloc.o \
  canopy_app.o
 
-ifeq ($(NETCDF), 0)
+ifeq ($(NC), 0)
   _ncf_objs := canopy_check_input.o canopy_ncf_io_mod.o
   OBJS := $(filter-out $(_ncf_objs),$(OBJS))
 endif

From 7a310693e20a797eca8aac7c46eb66e1278a1d31 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Fri, 9 Jun 2023 16:17:30 -0700
Subject: [PATCH 39/64] Update src/Makefile

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 src/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index c2cacd2f..11709748 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -36,7 +36,7 @@ endif
 # NETCDF Settings here
 LIBS :=
 INC :=
-$(info NETCDF setting: '$(NC)')
+$(info NC setting: '$(NC)')
 ifeq ($(NC), 1)
   NETCDF_FLIBS := $(shell nf-config --flibs)
   NETCDF_INC := -I$(shell nf-config --includedir)

From b21eba3051903816191077b04cf3cfb8370dd6b8 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Fri, 9 Jun 2023 16:22:24 -0700
Subject: [PATCH 40/64] Update src/Makefile

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 src/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index 11709748..f7666949 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -47,7 +47,7 @@ ifeq ($(NC), 1)
 else ifeq ($(NC), 0)
   #
 else
-  $(error invalid setting for NETCDF, should be 0 or 1 but is '$(NC)')
+  $(error invalid setting for NC, should be 0 or 1 but is '$(NC)')
 endif
 $(info LIBS: '$(LIBS)')
 $(info INC:  '$(INC)')

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 41/64] 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"

From facadbd38e3f1c70ef0cdab77954efd3cd5db194 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Sat, 10 Jun 2023 15:29:46 -0700
Subject: [PATCH 42/64] Update README.md- Edited for src/Makefile to build with
 both gfortran and ifort

---
 README.md | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 409f0e3e..ec0b7b42 100644
--- a/README.md
+++ b/README.md
@@ -19,13 +19,24 @@ Canopy-App requires NetCDF-Fortran Libraries (i.e., `-lnetcdf -lnetcdff`) when u
 See [the included Makefile](./src/Makefile), which detects NetCDF using `nf-config`, for an example (on GMU Hopper, you can use the `netcdf-c/4.7.4-vh` and `netcdf-fortran/4.5.3-ff` modules).
 
 Compilation options can be controlled with environment variables:
- - `DEBUG=0` (off; default) or `DEBUG=1` (on)
- - `NETCDF=0` (off) or `NETCDF=1` (on; default)
+
+- `FC=gfortran` (default) or ifort
+- `DEBUG=0` (off; default) or `DEBUG=1` (on)
+ - `NC=0` (off) or `NETCDF=1` (on; default)
 
 Example:
+a) with gfortran, Debug flags ON and with Netcdf:
+```
+DEBUG=1 NC=1 make -C src 
+```
+Note: Not supplying `FC` doesn't necessary give gfortran, since `FC` might already be set in the environment (such as, `module load` situations do this). On such case do:
+```
+DEBUG=1 NC=1 FC=gfortran make -C src 
 ```
-DEBUG=1 NETCDF=1 make -C src
+b) with ifort, Debug flags ON and with Netcdf:
 ```
+DEBUG=1 NC=1 FC=ifort make -C src
+``` 
 
 ### Modify settings
 

From 85f51d20fe88c3c69156a07ea44d125e2b224caa Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Sat, 10 Jun 2023 15:33:37 -0700
Subject: [PATCH 43/64] Update README.md (trailing whitespaces removed)

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index ec0b7b42..ab0d7d65 100644
--- a/README.md
+++ b/README.md
@@ -22,21 +22,21 @@ Compilation options can be controlled with environment variables:
 
 - `FC=gfortran` (default) or ifort
 - `DEBUG=0` (off; default) or `DEBUG=1` (on)
- - `NC=0` (off) or `NETCDF=1` (on; default)
+- `NC=0` (off) or `NETCDF=1` (on; default)
 
 Example:
 a) with gfortran, Debug flags ON and with Netcdf:
 ```
-DEBUG=1 NC=1 make -C src 
+DEBUG=1 NC=1 make -C src
 ```
 Note: Not supplying `FC` doesn't necessary give gfortran, since `FC` might already be set in the environment (such as, `module load` situations do this). On such case do:
 ```
-DEBUG=1 NC=1 FC=gfortran make -C src 
+DEBUG=1 NC=1 FC=gfortran make -C src
 ```
 b) with ifort, Debug flags ON and with Netcdf:
 ```
 DEBUG=1 NC=1 FC=ifort make -C src
-``` 
+```
 
 ### Modify settings
 

From 21689fa98146f033be2c1c8b6ca0547fc4f96b17 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Sat, 10 Jun 2023 15:38:01 -0700
Subject: [PATCH 44/64] Update README.md- Edited README.md to account for
 enhancement in src/Makefile to build Canopy-app with both ifort and gfortran

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ab0d7d65..46018811 100644
--- a/README.md
+++ b/README.md
@@ -25,11 +25,11 @@ Compilation options can be controlled with environment variables:
 - `NC=0` (off) or `NETCDF=1` (on; default)
 
 Example:
-a) with gfortran, Debug flags ON and with Netcdf:
+a) with gfortran, Debug flags ON and with Netcdf (if `echo $FC` gives gfortran):
 ```
 DEBUG=1 NC=1 make -C src
 ```
-Note: Not supplying `FC` doesn't necessary give gfortran, since `FC` might already be set in the environment (such as, `module load` situations do this). On such case do:
+Note: Not supplying `FC` doesn't necessary give gfortran, since `FC` might already be set in the environment (such as, `module load` situations do this). In such case do:
 ```
 DEBUG=1 NC=1 FC=gfortran make -C src
 ```

From 91365819d0f64ffadbfc7ee8de1ec9e0cdf93c9f Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Mon, 12 Jun 2023 14:31:41 -0700
Subject: [PATCH 45/64] Update README.md

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 46018811..50dd7cf0 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ Compilation options can be controlled with environment variables:
 - `NC=0` (off) or `NETCDF=1` (on; default)
 
 Example:
-a) with gfortran, Debug flags ON and with Netcdf (if `echo $FC` gives gfortran):
+a) with compiler set by `FC` environment variable (falling back to `gfortran` if unset), Debug flags ON and with NetCDF:
 ```
 DEBUG=1 NC=1 make -C src
 ```

From fe28540a3a99c2eb832d49795c60d9bc73b5925b Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Mon, 12 Jun 2023 14:32:05 -0700
Subject: [PATCH 46/64] Update README.md

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 50dd7cf0..419e4648 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ a) with compiler set by `FC` environment variable (falling back to `gfortran` if
 ```
 DEBUG=1 NC=1 make -C src
 ```
-Note: Not supplying `FC` doesn't necessary give gfortran, since `FC` might already be set in the environment (such as, `module load` situations do this). In such case do:
+Note: Not supplying `FC` doesn't necessarily give `gfortran`, since `FC` might already be set in the environment (for example, `module load` situations may do this). In such case do:
 ```
 DEBUG=1 NC=1 FC=gfortran make -C src
 ```

From 51e17cae97b3bf3aa598eb850e1550dce35e75a7 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Mon, 12 Jun 2023 14:32:31 -0700
Subject: [PATCH 47/64] Update README.md

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 419e4648..db51ed4d 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ Note: Not supplying `FC` doesn't necessarily give `gfortran`, since `FC` might a
 ```
 DEBUG=1 NC=1 FC=gfortran make -C src
 ```
-b) with ifort, Debug flags ON and with Netcdf:
+b) with Intel Fortran (`ifort`), Debug flags ON and with NetCDF:
 ```
 DEBUG=1 NC=1 FC=ifort make -C src
 ```

From 7d2b56d9349f3ef3c739001e355c41f9173ba5c3 Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Mon, 12 Jun 2023 14:36:36 -0700
Subject: [PATCH 48/64] Update src/Makefile (final revised ifort FCFLAGS)

Co-authored-by: Zachary Moon <zmoon92@gmail.com>
---
 src/Makefile | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index f7666949..1b65658f 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -22,10 +22,7 @@ ifeq ($(DEBUG), 1)
   ifeq ($(FC),gfortran)
     FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 -std=f2003 -fall-intrinsics
   else ifeq ($(FC),ifort)
-    # Tested the following Debug flag options on Hera with 'DEBUG=1 NC=1 FC=ifort make -C src'
-    # Both options build without warnings and also make clean in src
-    FCFLAGS := -g -warn all -implicitnone -O1 -error-limit 5  #Equivalent to gfortran Debug flags
-    #FCFLAGS  := -g -warn all -check bounds -traceback  #also builds Canopy-app on Hera with FC=ifort without warnings
+    FCFLAGS := -g -warn all -check bounds -implicitnone -O0 -error-limit 5
   endif
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3

From cd671636debba81aabf9ac07810020e760b0f89b Mon Sep 17 00:00:00 2001
From: quaz115 <63623865+quaz115@users.noreply.github.com>
Date: Mon, 12 Jun 2023 14:43:04 -0700
Subject: [PATCH 49/64] Update README.md (NETCDF to NC)

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

diff --git a/README.md b/README.md
index db51ed4d..648097b5 100644
--- a/README.md
+++ b/README.md
@@ -22,7 +22,7 @@ Compilation options can be controlled with environment variables:
 
 - `FC=gfortran` (default) or ifort
 - `DEBUG=0` (off; default) or `DEBUG=1` (on)
-- `NC=0` (off) or `NETCDF=1` (on; default)
+- `NC=0` (off) or `NC=1` (on; default)
 
 Example:
 a) with compiler set by `FC` environment variable (falling back to `gfortran` if unset), Debug flags ON and with NetCDF:

From 0ba97443f66c097b09472885023a96844fc69278 Mon Sep 17 00:00:00 2001
From: Wei-Ting Hung <107704243+angehung5@users.noreply.github.com>
Date: Wed, 28 Jun 2023 20:49:36 -0400
Subject: [PATCH 50/64] add frp_src=3

---
 python/global_data_process.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/python/global_data_process.py b/python/global_data_process.py
index 3bb33403..9f64347b 100755
--- a/python/global_data_process.py
+++ b/python/global_data_process.py
@@ -21,7 +21,7 @@
 houri = 12  # gfs initialization hour in UTC (caution: currently GFS input files are initialized at 12 UTC only -- do not change)
 hour = 0  # gfs forecast hour (0-24) in UTC
 ref_lev = 10  # reference height above the canopy (m)
-frp_src = 1  # frp data source for WAF (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
+frp_src = 1  # frp data source for WAF (0: local source; 1: check local source first, switch to climatological file if no available data; 2: 12 month climatology; 3: all ones when ifcanwaf=.FALSE.)
 
 
 # ---------------------------------ATTENTION---------------------------------#
@@ -390,6 +390,9 @@ def read_frp_local(filename, lat, lon, fill_value):
 
         if frp_src == 2:
             DATA = read_gfs_climatology(f_can, "frp")
+        elif frp_src == 3:
+            DATA = np.empty(lat.shape)
+            DATA[:] = 1
         else:
             DATA = read_frp_local(f_frp, lat, lon, fill_value)
 

From 357173879432759d015227e9ec3ea87bb324694e Mon Sep 17 00:00:00 2001
From: Wei-Ting Hung <107704243+angehung5@users.noreply.github.com>
Date: Thu, 29 Jun 2023 01:51:00 -0400
Subject: [PATCH 51/64] Update README.md

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

diff --git a/python/README.md b/python/README.md
index 22a45080..447ab8df 100644
--- a/python/README.md
+++ b/python/README.md
@@ -69,7 +69,7 @@ You can also download and generate global gridded canopy-app inputs using Python
    houri    = 12     # gfs initialization hour in UTC (caution currently GFS files are initialized at 12 UTC only -- do not change)
    hour     = 00     # gfs forecast hour in UTC
    ref_lev  = 10     # reference height above the canopy (m)
-   frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data ; 2: 12 month climatology)
+   frp_src  = 1      # frp data source (0: local source; 1: check local source first, switch to climatological file if no available data; 2: 12 month climatology; 3: all ones when ifcanwaf=.FALSE.)
    ```
 
 2. Activate canopy-app Conda environment:

From dcdd8afa8699542858bf5e498ba038d3dc905424 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Sun, 16 Jul 2023 13:21:31 -0400
Subject: [PATCH 52/64] Initial commit to start isolating tleaf_ppfd calcs.

---
 src/canopy_calcs.F90    | 17 +++++++++++++++++
 src/canopy_ppfd_mod.F90 |  6 +++---
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index e4aef172..867e21ed 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -137,6 +137,15 @@ SUBROUTINE canopy_calcs
                                 ubzref, z0ghc, lambdars, cdrag, pai, hcmref, hgtref, &
                                 z0ref, vtyperef, lu_opt, z0_opt, d_h, zo_h)
 
+! ... calculate canopy leaf temperature (sun/shade) profile
+
+
+! ... calculate canopy Photosynthetic Photon Flux Density (PPFD) (sun/shade) profile
+
+
+
+
+! ...                            **** User Canopy-App Options ***
 ! ... user option to calculate in-canopy wind speeds at height z and midflame WAF
 
                             if (ifcanwind .or. ifcanwaf) then
@@ -400,6 +409,14 @@ SUBROUTINE canopy_calcs
                             ubzref, z0ghc, lambdars, cdrag, pai, hcmref, hgtref, &
                             z0ref, vtyperef, lu_opt, z0_opt, d_h, zo_h)
 
+! ... calculate canopy leaf temperature (sun/shade) profile
+
+
+! ... calculate canopy Photosynthetic Photon Flux Density (PPFD) (sun/shade) profile
+
+
+! ...                            **** User Canopy-App Options ***
+
 ! ... user option to calculate in-canopy wind speeds at height z and midflame WAF
 
                         if (ifcanwind .or. ifcanwaf) then
diff --git a/src/canopy_ppfd_mod.F90 b/src/canopy_ppfd_mod.F90
index 0a270bda..8f86bd2d 100644
--- a/src/canopy_ppfd_mod.F90
+++ b/src/canopy_ppfd_mod.F90
@@ -10,7 +10,7 @@ SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
 !-----------------------------------------------------------------------
 
 ! Description:
-!     computes linear interpolation method for tleaf sun/shade in canopy.
+!     computes linear interpolation method for PPFD sun/shade in canopy.
 
 ! Preconditions:
 !     in-canopy height, and model LAI, clumping index, and solar zenith angle
@@ -19,8 +19,8 @@ SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
 
 ! Revision History:
 !     Prototype 06/23 by PCC
-!     Jun 2023 P.C. Campbell: Initial standalone tleaf linear subroutine based on
-!                             Silva et al. (2020) algorithms
+!     Jun 2023 P.C. Campbell: Initial standalone PPFD linear subroutine based on
+!                             Silva et al. (2020) exponential curve algorithms
 !-----------------------------------------------------------------------
 !-----------------------------------------------------------------------
         use canopy_const_mod, ONLY: RK     !constants for canopy models

From fdef150482472ba4e5baaa325b89e1027bfca890 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Thu, 20 Jul 2023 12:52:24 -0400
Subject: [PATCH 53/64] Added new radiation/fsun routine and other changes.

---
 src/Makefile               |  1 +
 src/canopy_alloc.F90       |  3 +++
 src/canopy_bioemi_mod.F90  | 17 ++++++++++++++
 src/canopy_calcs.F90       | 23 ++++++++++++++++---
 src/canopy_canvars_mod.F90 |  3 +++
 src/canopy_dealloc.F90     |  3 +++
 src/canopy_init.F90        |  3 +++
 src/canopy_ppfd_mod.F90    |  6 ++++-
 src/canopy_rad_mod.F90     | 47 ++++++++++++++++++++++++++++++++++++++
 src/canopy_tleaf_mod.F90   |  6 ++++-
 10 files changed, 107 insertions(+), 5 deletions(-)
 create mode 100644 src/canopy_rad_mod.F90

diff --git a/src/Makefile b/src/Makefile
index e2d99194..0ffe4008 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -68,6 +68,7 @@ OBJS :=\
  canopy_dxcalc_mod.o \
  canopy_profile_mod.o \
  canopy_phot_mod.o \
+ canopy_rad_mod.o \
  canopy_ppfd_mod.o \
  canopy_tleaf_mod.o \
  canopy_wind_mod.o \
diff --git a/src/canopy_alloc.F90 b/src/canopy_alloc.F90
index ba007672..517de2bf 100644
--- a/src/canopy_alloc.F90
+++ b/src/canopy_alloc.F90
@@ -27,10 +27,13 @@ SUBROUTINE canopy_alloc
 
     if(.not.allocated(zhc))         allocate(zhc(modlays))
     if(.not.allocated(fafraczInt))  allocate(fafraczInt(modlays))
+    if(.not.allocated(fsun))        allocate(fsun(modlays))
     if(.not.allocated(tleaf_sun))   allocate(tleaf_sun(modlays))
     if(.not.allocated(tleaf_shade)) allocate(tleaf_shade(modlays))
+    if(.not.allocated(tleaf_ave))   allocate(tleaf_ave(modlays))
     if(.not.allocated(ppfd_sun))    allocate(ppfd_sun(modlays))
     if(.not.allocated(ppfd_shade))  allocate(ppfd_shade(modlays))
+    if(.not.allocated(ppfd_ave))    allocate(ppfd_ave(modlays))
 
 !-------------------------------------------------------------------------------
 ! Allocate arrays for Canopy Wind Outputs
diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index ba3d87d2..b8889b57 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -30,6 +30,8 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 !-----------------------------------------------------------------------
 !     Jan 2023 P.C. Campbell: Initial canopy isoprene only version
 !     Feb 2023 P.C. Campbell: Modified for multiple biogenic species
+!     Jul 2023 P.C. Campbell: Restructured to use FSUN, TLEAF, and PPFD
+!                             as inputs
 !-----------------------------------------------------------------------
 !-----------------------------------------------------------------------
         use canopy_const_mod, ONLY: rk,rgasuniv   !constants for canopy models
@@ -42,12 +44,15 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),    INTENT( IN )       :: ZK(:)           ! Input model heights (m)
         REAL(RK),    INTENT( IN )       :: FCLAI(:)        ! Input Fractional (z) shapes of the
         ! plant surface distribution (nondimensional), i.e., a Fractional Culmulative LAI
+!add....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE, PPFD_SUN, PPFD_SHADE
         REAL(RK),    INTENT( IN )       :: FCH             ! Model input canopy height (m)
         REAL(RK),    INTENT( IN )       :: LAI             ! Model input total Leaf Area Index
+!---------comment out
         REAL(RK),    INTENT( IN )       :: CLU             ! Model input Clumping Index
         REAL(RK),    INTENT( IN )       :: COSZEN          ! Model input Cosine Solar Zenith Angle
         REAL(RK),    INTENT( IN )       :: SFCRAD          ! Model input Instantaneous surface downward shortwave flux (W/m2)
         REAL(RK),    INTENT( IN )       :: TEMP2           ! Model input 2-m Temperature (K)
+!---------
         INTEGER,     INTENT( IN )       :: LU_OPT          ! integer for LU type from model mapped to Massman et al. (default = 0/VIIRS)
         INTEGER,     INTENT( IN )       :: VTYPE           ! Grid cell dominant vegetation type
         REAL(RK),    INTENT( IN )       :: MODRES          ! Canopy model input vertical resolution (m)
@@ -59,6 +64,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),    INTENT( OUT )      :: EMI_OUT(:)      ! Output canopy layer volume emissions (kg m-3 s-1)
 
 ! Local Variables
+!---------comment out
         REAL(RK) :: FSUN(SIZE(ZK))                 ! Sunlit/Shaded fraction from photolysis correction factor
         REAL(RK) :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
         REAL(RK) :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
@@ -73,6 +79,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK) :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
         REAL(RK) :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
         REAL(RK) :: TLEAF_AVE(SIZE(ZK))            ! Average Leaf temp (K)
+!-------------
         REAL(RK) :: TLEAF24_AVE(SIZE(ZK))          ! Average Leaf temp over the past 24 hours (K)
         REAL(RK) :: TLEAF240_AVE(SIZE(ZK))         ! Average Leaf temp over the past 240 hours (K)
         REAL(RK) :: GammaTLEAF_SUN_NUM(SIZE(ZK))   ! Numerator in Tleaf sun activity factor
@@ -108,6 +115,8 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
         REAL(RK),          PARAMETER     :: PPFD0_SUN       =  200.0      !Constant PPFDo sunlit (umol/m2 s) (Guenther et al.,2012)
         REAL(RK),          PARAMETER     :: PPFD0_SHADE     =  50.0       !Constant PPFDo shaded (umol/m2 s) (Guenther et al.,2012)
+
+!----------------comment out
         REAL(RK),          PARAMETER     :: ATEMP_1_SUN     =  -13.891_rk !Linearized 2-m temp --> leaf temp parameters (Level 1 =
         !top of canopy
         REAL(RK),          PARAMETER     :: ATEMP_2_SUN     =  -12.322_rk !Based on Table 1 in Silva et al. (2022)
@@ -150,9 +159,13 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
         REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
         REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
+!------------
+
 
         REAL(RK),          PARAMETER     :: CT2             =  230.0_rk   !Deactivation energy (kJ/mol) (Guenther et al., 2012)
 
+
+!------------comment out
 !Calculate photolyis shading/correction factor through canopy, i.e., the fraction of sunlit leaves downward through canopy
 !  `canopy_phot` gives relative direct beam irradiance,
 !  which, multiplied by clumping index, gives sunlit fraction (e.g., Bonan 2019, eq. 14.18)
@@ -268,6 +281,10 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
         PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
         PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
+!----------------
+
+!Start here for biogenic calculations needed in model....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE
+        !PPFD_SUN, PPFD_SHADE
 
 ! Calculate maximum normalized emission capacity (E_OPT) and Tleaf at E_OPT
         TLEAF240_AVE   = TLEAF_AVE  !Assume instantaneous TLEAF estimate for TLEAF240 and TLEAF24 (could improve...)
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 867e21ed..477f33f6 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -15,7 +15,10 @@ SUBROUTINE canopy_calcs
     use canopy_utils_mod      !main canopy utilities
     use canopy_dxcalc_mod     !main canopy dx calculation
     use canopy_profile_mod    !main canopy foliage profile routines
-    use canopy_wind_mod       !main canopy wind components
+    use canopy_rad_mod        !main canopy radiation sunlit/shaded routines
+    use canopy_tleaf_mod      !main canopy leaf temperature optons
+    use canopy_ppfd_mod       !main canopy leaf PPFD optons
+    use canopy_wind_mod       !main canopy components
     use canopy_waf_mod
     use canopy_phot_mod
     use canopy_eddy_mod
@@ -137,13 +140,19 @@ SUBROUTINE canopy_calcs
                                 ubzref, z0ghc, lambdars, cdrag, pai, hcmref, hgtref, &
                                 z0ref, vtyperef, lu_opt, z0_opt, d_h, zo_h)
 
-! ... calculate canopy leaf temperature (sun/shade) profile
+! ... calculate canopy radiation (sunlit and shade) profile
 
+                            call canopy_fsun_clu( fafraczInt, lairef, cluref, cszref, fsun)
 
-! ... calculate canopy Photosynthetic Photon Flux Density (PPFD) (sun/shade) profile
+! ... calculate canopy leaf temperature (sun/shade) profile
 
+                            call canopy_tleaf_lin(zk, hcmref, tmp2mref, fsun, &
+                                tleaf_sun, tleaf_shade, tleaf_ave)
 
+! ... calculate canopy Photosynthetic Photon Flux Density (PPFD) (sun/shade) profile
 
+                            call canopy_ppfd_exp(zk, hcmref, dswrfref, lairef, fsun, &
+                                ppfd_sun, ppfd_shade, ppfd_ave)
 
 ! ...                            **** User Canopy-App Options ***
 ! ... user option to calculate in-canopy wind speeds at height z and midflame WAF
@@ -409,11 +418,19 @@ SUBROUTINE canopy_calcs
                             ubzref, z0ghc, lambdars, cdrag, pai, hcmref, hgtref, &
                             z0ref, vtyperef, lu_opt, z0_opt, d_h, zo_h)
 
+! ... calculate canopy radiation (sunlit and shade) profile
+
+                        call canopy_fsun_clu( fafraczInt, lairef, cluref, cszref, fsun)
+
 ! ... calculate canopy leaf temperature (sun/shade) profile
 
+                        call canopy_tleaf_lin(zk, hcmref, tmp2mref, fsun, &
+                            tleaf_sun, tleaf_shade, tleaf_ave)
 
 ! ... calculate canopy Photosynthetic Photon Flux Density (PPFD) (sun/shade) profile
 
+                        call canopy_ppfd_exp(zk, hcmref, dswrfref, lairef, fsun, &
+                            ppfd_sun, ppfd_shade, ppfd_ave)
 
 ! ...                            **** User Canopy-App Options ***
 
diff --git a/src/canopy_canvars_mod.F90 b/src/canopy_canvars_mod.F90
index 1c5ff989..5519e1f2 100644
--- a/src/canopy_canvars_mod.F90
+++ b/src/canopy_canvars_mod.F90
@@ -33,10 +33,13 @@ MODULE canopy_canvars_mod
     real(rk), allocatable :: fainc         ( : )          ! incremental foliage shape function
     real(rk), allocatable :: fafracz       ( : )          ! incremental fractional foliage shape function
     real(rk), allocatable :: fafraczInt    ( : )          ! integral of incremental fractional foliage shape function
+    real(rk), allocatable :: fsun          ( : )          ! Sunlit/Shaded fraction from photolysis correction factor
     real(rk), allocatable :: tleaf_sun     ( : )          ! Leaf temp for sunlit leaves (K)
     real(rk), allocatable :: tleaf_shade   ( : )          ! Leaf temp for shaded leaves (K)
+    real(rk), allocatable :: tleaf_ave     ( : )          ! Average Leaf temp for sunlit and shaded leaves (K)
     real(rk), allocatable :: ppfd_sun      ( : )          ! PPFD for sunlit leaves (umol phot/m2 s)
     real(rk), allocatable :: ppfd_shade    ( : )          ! PPFD for shaded leaves (umol phot/m2 s)
+    real(rk), allocatable :: ppfd_ave      ( : )          ! Average PPFD for sunlit and shaded leaves (umol phot/m2 s)
     real(rk), allocatable :: canBOT        ( : )          ! Canopy bottom wind reduction factors
     real(rk), allocatable :: canTOP        ( : )          ! Canopy top wind reduction factors
     real(rk), allocatable :: canWIND       ( : , : )      ! canopy wind speeds (m/s)
diff --git a/src/canopy_dealloc.F90 b/src/canopy_dealloc.F90
index 6a65359b..29f015bc 100644
--- a/src/canopy_dealloc.F90
+++ b/src/canopy_dealloc.F90
@@ -30,10 +30,13 @@ SUBROUTINE canopy_dealloc
     if(allocated(fainc))       deallocate(fainc) !allocated in canopy_profile
     if(allocated(fafracz))     deallocate(fafracz) !allocated in canopy_profile
     if(allocated(fafraczInt))  deallocate(fafraczInt)
+    if(allocated(fsun))        deallocate(fsun)
     if(allocated(tleaf_sun))   deallocate(tleaf_sun)
     if(allocated(tleaf_shade)) deallocate(tleaf_shade)
+    if(allocated(tleaf_ave))   deallocate(tleaf_ave)
     if(allocated(ppfd_sun))    deallocate(ppfd_sun)
     if(allocated(ppfd_shade))  deallocate(ppfd_shade)
+    if(allocated(ppfd_ave))    deallocate(ppfd_ave)
 
 !-------------------------------------------------------------------------------
 ! Deallocate arrays for Canopy Wind
diff --git a/src/canopy_init.F90 b/src/canopy_init.F90
index bda4345f..9a0bfa34 100644
--- a/src/canopy_init.F90
+++ b/src/canopy_init.F90
@@ -21,10 +21,13 @@ SUBROUTINE canopy_init
 
     if(allocated(zhc))          zhc(:)         = fillreal
     if(allocated(fafraczInt))   fafraczInt(:)  = fillreal
+    if(allocated(fsun))         fsun(:)        = fillreal
     if(allocated(tleaf_sun))    tleaf_sun(:)   = fillreal
     if(allocated(tleaf_shade))  tleaf_shade(:) = fillreal
+    if(allocated(tleaf_ave))    tleaf_ave(:)   = fillreal
     if(allocated(ppfd_sun))     ppfd_sun(:)    = fillreal
     if(allocated(ppfd_shade))   ppfd_shade(:)  = fillreal
+    if(allocated(ppfd_ave))   ppfd_ave(:)      = fillreal
 
 !-------------------------------------------------------------------------------
 ! Initialize arrays for Canopy Wind
diff --git a/src/canopy_ppfd_mod.F90 b/src/canopy_ppfd_mod.F90
index 8f86bd2d..37582b9f 100644
--- a/src/canopy_ppfd_mod.F90
+++ b/src/canopy_ppfd_mod.F90
@@ -5,7 +5,8 @@ module canopy_ppfd_mod
 contains
 
 !:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-    SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
+    SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, FSUN, &
+        PPFD_SUN, PPFD_SHADE, PPFD_AVE)
 
 !-----------------------------------------------------------------------
 
@@ -32,8 +33,10 @@ SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
         REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
         REAL(RK),    INTENT( IN )       :: SFCRAD                         ! Model input Instantaneous surface downward shortwave flux (W/m2)
         REAL(RK),    INTENT( IN )       :: LAI                            ! Model input total Leaf Area Index
+        REAL(RK),    INTENT( IN )       :: FSUN(:)                        ! Sunlit/Shaded fraction from photolysis correction factor
         REAL(RK),    INTENT( OUT )      :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
         REAL(RK),    INTENT( OUT )      :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( OUT )      :: PPFD_AVE(SIZE(ZK))             ! Average PPFD for sunlit and shaded leaves (umol phot/m2 s)
 
 !      LOCAL
         REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
@@ -120,6 +123,7 @@ SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, PPFD_SUN, PPFD_SHADE)
 
         PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
         PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
+        PPFD_AVE = (PPFD_SUN*FSUN) + (PPFD_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
 
     END SUBROUTINE CANOPY_PPFD_EXP
 
diff --git a/src/canopy_rad_mod.F90 b/src/canopy_rad_mod.F90
new file mode 100644
index 00000000..579cc183
--- /dev/null
+++ b/src/canopy_rad_mod.F90
@@ -0,0 +1,47 @@
+module canopy_rad_mod
+
+    implicit none
+
+contains
+
+!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+    SUBROUTINE CANOPY_FSUN_CLU( FCLAI, LAI, CLU, COSZEN, FSUN)
+
+!-----------------------------------------------------------------------
+
+! Description:
+!     computes linear interpolation method for PPFD sun/shade in canopy.
+
+! Preconditions:
+!     in-canopy height, and model LAI, clumping index, and solar zenith angle
+
+! Subroutines and Functions Called:
+
+! Revision History:
+!     Prototype 06/23 by PCC
+!     Jun 2023 P.C. Campbell: Initial standalone PPFD linear subroutine based on
+!                             Silva et al. (2020) exponential curve algorithms
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+        use canopy_const_mod, ONLY: RK     !constants for canopy models
+        use canopy_phot_mod
+
+! Arguments:
+!     IN/OUT
+        REAL(RK),    INTENT( IN )       :: FCLAI(:)          ! Input Fractional (z) shapes of the
+        ! plant surface distribution (nondimensional), i.e., a Fractional Culmulative LAI
+        REAL(RK),    INTENT( IN )       :: LAI               ! Model input total Leaf Area Index
+        REAL(RK),    INTENT( IN )       :: CLU               ! Model input Clumping Index
+        REAL(RK),    INTENT( IN )       :: COSZEN            ! Model input Cosine Solar Zenith Angle
+        REAL(RK),    INTENT( OUT )      :: FSUN(SIZE(FCLAI)) ! Sunlit/Shaded fraction from photolysis correction factor
+
+!Calculate photolyis shading/correction factor through canopy, i.e., the fraction of sunlit leaves downward through canopy
+!  `canopy_phot` gives relative direct beam irradiance,
+!  which, multiplied by clumping index, gives sunlit fraction (e.g., Bonan 2019, eq. 14.18)
+
+        call canopy_phot(FCLAI, LAI, CLU, COSZEN, FSUN)
+        FSUN = FSUN * CLU
+
+    END SUBROUTINE CANOPY_FSUN_CLU
+
+end module canopy_rad_mod
diff --git a/src/canopy_tleaf_mod.F90 b/src/canopy_tleaf_mod.F90
index a5c172dd..aac93106 100644
--- a/src/canopy_tleaf_mod.F90
+++ b/src/canopy_tleaf_mod.F90
@@ -5,7 +5,8 @@ module canopy_tleaf_mod
 contains
 
 !:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-    SUBROUTINE CANOPY_TLEAF_LIN( ZK, FCH, TEMP2, TLEAF_SUN, TLEAF_SHADE)
+    SUBROUTINE CANOPY_TLEAF_LIN( ZK, FCH, TEMP2, FSUN, &
+        TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE)
 
 !-----------------------------------------------------------------------
 
@@ -31,8 +32,10 @@ SUBROUTINE CANOPY_TLEAF_LIN( ZK, FCH, TEMP2, TLEAF_SUN, TLEAF_SHADE)
         REAL(RK),    INTENT( IN )       :: ZK(:)                          ! Input model heights (m)
         REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
         REAL(RK),    INTENT( IN )       :: TEMP2                          ! Model input 2-m Temperature (K
+        REAL(RK),    INTENT( IN )       :: FSUN(:)                        ! Sunlit/Shaded fraction from photolysis correction factor
         REAL(RK),    INTENT( OUT )      :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
         REAL(RK),    INTENT( OUT )      :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
+        REAL(RK),    INTENT( OUT )      :: TLEAF_AVE(SIZE(ZK))            ! Ave Leaf temp for sun/shaded leaves (K)
 
 !      LOCAL
         !Linearized 2-m temp --> leaf temp parameters Based on Table 1 in Silva et al. (2020)
@@ -116,6 +119,7 @@ SUBROUTINE CANOPY_TLEAF_LIN( ZK, FCH, TEMP2, TLEAF_SUN, TLEAF_SHADE)
 
         TLEAF_SUN   = ATEMP_SUN + (BTEMP_SUN*TEMP2)
         TLEAF_SHADE = ATEMP_SHADE + (BTEMP_SHADE*TEMP2)
+        TLEAF_AVE = (TLEAF_SUN*FSUN) + (TLEAF_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
 
     END SUBROUTINE CANOPY_TLEAF_LIN
 

From 58835663a01c83549a67cef62b2b9365c1a51eeb Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 21 Jul 2023 16:11:30 -0400
Subject: [PATCH 54/64] Updates to bioemi and main calcs for new inputs.

---
 src/canopy_bioemi_mod.F90 | 375 ++++++++++++++++++++------------------
 src/canopy_calcs.F90      | 114 ++++++++----
 2 files changed, 270 insertions(+), 219 deletions(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index b8889b57..228164ab 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -5,10 +5,15 @@ module canopy_bioemi_mod
 contains
 
 !:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-    SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
-        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
+    SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
+        PPFD_SHADE, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE, LU_OPT, &
+        VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
         EMI_IND, EMI_OUT)
 
+!    SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
+!        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
+!        EMI_IND, EMI_OUT)
+
 !-----------------------------------------------------------------------
 
 ! Description:
@@ -41,17 +46,25 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
 ! Arguments:
 !     IN/OUT
-        REAL(RK),    INTENT( IN )       :: ZK(:)           ! Input model heights (m)
-        REAL(RK),    INTENT( IN )       :: FCLAI(:)        ! Input Fractional (z) shapes of the
+        REAL(RK),    INTENT( IN )       :: ZK(:)           ! Model heights (m)
+        REAL(RK),    INTENT( IN )       :: FCLAI(:)        ! Fractional (z) shapes of the
         ! plant surface distribution (nondimensional), i.e., a Fractional Culmulative LAI
 !add....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE, PPFD_SUN, PPFD_SHADE
-        REAL(RK),    INTENT( IN )       :: FCH             ! Model input canopy height (m)
-        REAL(RK),    INTENT( IN )       :: LAI             ! Model input total Leaf Area Index
+        REAL(RK),    INTENT( IN )       :: FCH             ! Ccanopy height (m)
+        REAL(RK),    INTENT( IN )       :: LAI             ! Total Leaf Area Index
+        REAL(RK),    INTENT( IN )       :: FSUN(:)         ! Sunlit/Shaded fraction from photolysis correction factor
+        REAL(RK),    INTENT( IN )       :: PPFD_SUN(:)     ! PPFD for sunlit leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( IN )       :: PPFD_SHADE(:)   ! PPFD for shaded leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( IN )       :: TLEAF_SUN(:)    ! Leaf temp for sunlit leaves (K)
+        REAL(RK),    INTENT( IN )       :: TLEAF_SHADE(:)  ! Leaf temp for shaded leaves (K)
+        REAL(RK),    INTENT( IN )       :: TLEAF_AVE(:)    ! Average Leaf temp (K)
+
+
 !---------comment out
-        REAL(RK),    INTENT( IN )       :: CLU             ! Model input Clumping Index
-        REAL(RK),    INTENT( IN )       :: COSZEN          ! Model input Cosine Solar Zenith Angle
-        REAL(RK),    INTENT( IN )       :: SFCRAD          ! Model input Instantaneous surface downward shortwave flux (W/m2)
-        REAL(RK),    INTENT( IN )       :: TEMP2           ! Model input 2-m Temperature (K)
+!        REAL(RK),    INTENT( IN )       :: CLU             ! Model input Clumping Index
+!        REAL(RK),    INTENT( IN )       :: COSZEN          ! Model input Cosine Solar Zenith Angle
+!        REAL(RK),    INTENT( IN )       :: SFCRAD          ! Model input Instantaneous surface downward shortwave flux (W/m2)
+!        REAL(RK),    INTENT( IN )       :: TEMP2           ! Model input 2-m Temperature (K)
 !---------
         INTEGER,     INTENT( IN )       :: LU_OPT          ! integer for LU type from model mapped to Massman et al. (default = 0/VIIRS)
         INTEGER,     INTENT( IN )       :: VTYPE           ! Grid cell dominant vegetation type
@@ -65,20 +78,20 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
 ! Local Variables
 !---------comment out
-        REAL(RK) :: FSUN(SIZE(ZK))                 ! Sunlit/Shaded fraction from photolysis correction factor
-        REAL(RK) :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
-        REAL(RK) :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
-        REAL(RK) :: ATEMP_SUN(SIZE(ZK))            ! Regression coefficient A for sun leaves (Silva et al., 2020)
-        REAL(RK) :: BTEMP_SUN(SIZE(ZK))            ! Regression coefficient B for sun leaves
-        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
-        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
-        REAL(RK) :: ATEMP_SHADE(SIZE(ZK))          ! Regression coefficient A for shade leaves
-        REAL(RK) :: BTEMP_SHADE(SIZE(ZK))          ! Regression coefficient B for shade leaves
-        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
-        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
-        REAL(RK) :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
-        REAL(RK) :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
-        REAL(RK) :: TLEAF_AVE(SIZE(ZK))            ! Average Leaf temp (K)
+!        REAL(RK) :: FSUN(SIZE(ZK))                 ! Sunlit/Shaded fraction from photolysis correction factor
+!        REAL(RK) :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
+!        REAL(RK) :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
+!        REAL(RK) :: ATEMP_SUN(SIZE(ZK))            ! Regression coefficient A for sun leaves (Silva et al., 2020)
+!        REAL(RK) :: BTEMP_SUN(SIZE(ZK))            ! Regression coefficient B for sun leaves
+!        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
+!        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
+!        REAL(RK) :: ATEMP_SHADE(SIZE(ZK))          ! Regression coefficient A for shade leaves
+!        REAL(RK) :: BTEMP_SHADE(SIZE(ZK))          ! Regression coefficient B for shade leaves
+!        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
+!        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
+!        REAL(RK) :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
+!        REAL(RK) :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
+!        REAL(RK) :: TLEAF_AVE(SIZE(ZK))            ! Average Leaf temp (K)
 !-------------
         REAL(RK) :: TLEAF24_AVE(SIZE(ZK))          ! Average Leaf temp over the past 24 hours (K)
         REAL(RK) :: TLEAF240_AVE(SIZE(ZK))         ! Average Leaf temp over the past 240 hours (K)
@@ -117,48 +130,48 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
         REAL(RK),          PARAMETER     :: PPFD0_SHADE     =  50.0       !Constant PPFDo shaded (umol/m2 s) (Guenther et al.,2012)
 
 !----------------comment out
-        REAL(RK),          PARAMETER     :: ATEMP_1_SUN     =  -13.891_rk !Linearized 2-m temp --> leaf temp parameters (Level 1 =
-        !top of canopy
-        REAL(RK),          PARAMETER     :: ATEMP_2_SUN     =  -12.322_rk !Based on Table 1 in Silva et al. (2022)
-        REAL(RK),          PARAMETER     :: ATEMP_3_SUN     =  -1.032_rk  !
-        REAL(RK),          PARAMETER     :: ATEMP_4_SUN     =  -5.172_rk  !
-        REAL(RK),          PARAMETER     :: ATEMP_5_SUN     =  -5.589_rk  !...
-        REAL(RK),          PARAMETER     :: BTEMP_1_SUN     =  1.064_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_2_SUN     =  1.057_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_3_SUN     =  1.031_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_4_SUN     =  1.050_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_5_SUN     =  1.051_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
-        !top of canopy
-        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
-        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
-        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
-        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
-        REAL(RK),          PARAMETER     :: ATEMP_1_SHADE   =  -12.846_rk !...
-        REAL(RK),          PARAMETER     :: ATEMP_2_SHADE   =  -11.343_rk !...
-        REAL(RK),          PARAMETER     :: ATEMP_3_SHADE   =  -1.068_rk  !...
-        REAL(RK),          PARAMETER     :: ATEMP_4_SHADE   =  -5.551_rk  !...
-        REAL(RK),          PARAMETER     :: ATEMP_5_SHADE   =  -5.955_rk  !...
-        REAL(RK),          PARAMETER     :: BTEMP_1_SHADE   =  1.060_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_2_SHADE   =  1.053_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_3_SHADE   =  1.031_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_4_SHADE   =  1.051_rk   !...
-        REAL(RK),          PARAMETER     :: BTEMP_5_SHADE   =  1.053_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
+!        REAL(RK),          PARAMETER     :: ATEMP_1_SUN     =  -13.891_rk !Linearized 2-m temp --> leaf temp parameters (Level 1 =
+!        !top of canopy
+!        REAL(RK),          PARAMETER     :: ATEMP_2_SUN     =  -12.322_rk !Based on Table 1 in Silva et al. (2022)
+!        REAL(RK),          PARAMETER     :: ATEMP_3_SUN     =  -1.032_rk  !
+!        REAL(RK),          PARAMETER     :: ATEMP_4_SUN     =  -5.172_rk  !
+!        REAL(RK),          PARAMETER     :: ATEMP_5_SUN     =  -5.589_rk  !...
+!        REAL(RK),          PARAMETER     :: BTEMP_1_SUN     =  1.064_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_2_SUN     =  1.057_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_3_SUN     =  1.031_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_4_SUN     =  1.050_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_5_SUN     =  1.051_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
+!        !top of canopy
+!        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
+!        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
+!        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
+!        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
+!        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
+!        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
+!        REAL(RK),          PARAMETER     :: ATEMP_1_SHADE   =  -12.846_rk !...
+!        REAL(RK),          PARAMETER     :: ATEMP_2_SHADE   =  -11.343_rk !...
+!        REAL(RK),          PARAMETER     :: ATEMP_3_SHADE   =  -1.068_rk  !...
+!        REAL(RK),          PARAMETER     :: ATEMP_4_SHADE   =  -5.551_rk  !...
+!        REAL(RK),          PARAMETER     :: ATEMP_5_SHADE   =  -5.955_rk  !...
+!        REAL(RK),          PARAMETER     :: BTEMP_1_SHADE   =  1.060_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_2_SHADE   =  1.053_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_3_SHADE   =  1.031_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_4_SHADE   =  1.051_rk   !...
+!        REAL(RK),          PARAMETER     :: BTEMP_5_SHADE   =  1.053_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
+!        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
+!        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
+!        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
+!        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
 !------------
 
 
@@ -166,121 +179,121 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
 
 
 !------------comment out
-!Calculate photolyis shading/correction factor through canopy, i.e., the fraction of sunlit leaves downward through canopy
-!  `canopy_phot` gives relative direct beam irradiance,
-!  which, multiplied by clumping index, gives sunlit fraction (e.g., Bonan 2019, eq. 14.18)
-
-        call canopy_phot(FCLAI, LAI, CLU, COSZEN, FSUN)
-        FSUN = FSUN * CLU
-
-! Use linear canopy temperature model based on Silva et al. (2020) to get approx. sun/shade leaf temperatures
-! through canopy (ignores effect of wind speed on leaf boundary layer ~ 1 % error/bias)
-!Citation:
-!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
-!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
-!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
-        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
-            if (ZK(i) .gt. FCH) then ! above canopy, Tleaf = Tair
-                ATEMP_SUN(i)   = 0.0
-                BTEMP_SUN(i)   = 1.0
-                ATEMP_SHADE(i) = 0.0
-                BTEMP_SHADE(i) = 1.0
-            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
-                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ ATEMP_2_SUN,ATEMP_1_SUN /),ZK(i))
-                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ BTEMP_2_SUN,BTEMP_1_SUN /),ZK(i))
-                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ ATEMP_2_SHADE,ATEMP_1_SHADE /),ZK(i))
-                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ BTEMP_2_SHADE,BTEMP_1_SHADE /),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
-                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ ATEMP_3_SUN,ATEMP_2_SUN /),ZK(i))
-                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ BTEMP_3_SUN,BTEMP_2_SUN /),ZK(i))
-                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ ATEMP_3_SHADE,ATEMP_2_SHADE /),ZK(i))
-                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ BTEMP_3_SHADE,BTEMP_2_SHADE /),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
-                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ ATEMP_4_SUN,ATEMP_3_SUN /),ZK(i))
-                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ BTEMP_4_SUN,BTEMP_3_SUN /),ZK(i))
-                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ ATEMP_4_SHADE,ATEMP_3_SHADE /),ZK(i))
-                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ BTEMP_4_SHADE,BTEMP_3_SHADE /),ZK(i))
-            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
-                ATEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ ATEMP_5_SUN,ATEMP_4_SUN /),ZK(i))
-                BTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ BTEMP_5_SUN,BTEMP_4_SUN /),ZK(i))
-                ATEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ ATEMP_5_SHADE,ATEMP_4_SHADE /),ZK(i))
-                BTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ BTEMP_5_SHADE,BTEMP_4_SHADE /),ZK(i))
-            end if
-        end do
-
-        TLEAF_SUN   = ATEMP_SUN + (BTEMP_SUN*TEMP2)
-        TLEAF_SHADE = ATEMP_SHADE + (BTEMP_SHADE*TEMP2)
-        TLEAF_AVE = (TLEAF_SUN*FSUN) + (TLEAF_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
-
-! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
-! through canopy
-!Citation:
-!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
-!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
-!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
-        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
-            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
-                CTEMP_SUN(i)   = 0.0
-                DTEMP_SUN(i)   = 0.0
-                CTEMP_SHADE(i) = 0.0
-                DTEMP_SHADE(i) = 0.0
-            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
-            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
-                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
-            end if
-        end do
-
-        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
-        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
+!!Calculate photolyis shading/correction factor through canopy, i.e., the fraction of sunlit leaves downward through canopy
+!!  `canopy_phot` gives relative direct beam irradiance,
+!!  which, multiplied by clumping index, gives sunlit fraction (e.g., Bonan 2019, eq. 14.18)
+!
+!        call canopy_phot(FCLAI, LAI, CLU, COSZEN, FSUN)
+!        FSUN = FSUN * CLU
+!
+!! Use linear canopy temperature model based on Silva et al. (2020) to get approx. sun/shade leaf temperatures
+!! through canopy (ignores effect of wind speed on leaf boundary layer ~ 1 % error/bias)
+!!Citation:
+!!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
+!!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
+!!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
+!        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
+!            if (ZK(i) .gt. FCH) then ! above canopy, Tleaf = Tair
+!                ATEMP_SUN(i)   = 0.0
+!                BTEMP_SUN(i)   = 1.0
+!                ATEMP_SHADE(i) = 0.0
+!                BTEMP_SHADE(i) = 1.0
+!            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ ATEMP_2_SUN,ATEMP_1_SUN /),ZK(i))
+!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ BTEMP_2_SUN,BTEMP_1_SUN /),ZK(i))
+!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ ATEMP_2_SHADE,ATEMP_1_SHADE /),ZK(i))
+!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ BTEMP_2_SHADE,BTEMP_1_SHADE /),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
+!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_3_SUN,ATEMP_2_SUN /),ZK(i))
+!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_3_SUN,BTEMP_2_SUN /),ZK(i))
+!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_3_SHADE,ATEMP_2_SHADE /),ZK(i))
+!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_3_SHADE,BTEMP_2_SHADE /),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
+!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_4_SUN,ATEMP_3_SUN /),ZK(i))
+!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_4_SUN,BTEMP_3_SUN /),ZK(i))
+!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_4_SHADE,ATEMP_3_SHADE /),ZK(i))
+!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_4_SHADE,BTEMP_3_SHADE /),ZK(i))
+!            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+!                ATEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_5_SUN,ATEMP_4_SUN /),ZK(i))
+!                BTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_5_SUN,BTEMP_4_SUN /),ZK(i))
+!                ATEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ ATEMP_5_SHADE,ATEMP_4_SHADE /),ZK(i))
+!                BTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ BTEMP_5_SHADE,BTEMP_4_SHADE /),ZK(i))
+!            end if
+!        end do
+!
+!        TLEAF_SUN   = ATEMP_SUN + (BTEMP_SUN*TEMP2)
+!        TLEAF_SHADE = ATEMP_SHADE + (BTEMP_SHADE*TEMP2)
+!        TLEAF_AVE = (TLEAF_SUN*FSUN) + (TLEAF_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
+!
+!! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
+!! through canopy
+!!Citation:
+!!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
+!!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
+!!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
+!        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
+!            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
+!                CTEMP_SUN(i)   = 0.0
+!                DTEMP_SUN(i)   = 0.0
+!                CTEMP_SHADE(i) = 0.0
+!                DTEMP_SHADE(i) = 0.0
+!            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
+!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
+!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
+!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+!                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
+!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
+!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
+!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
+!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
+!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
+!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
+!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
+!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
+!            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+!                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
+!                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
+!                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
+!                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+!                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
+!            end if
+!        end do
+!
+!        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
+!        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
 !----------------
 
 !Start here for biogenic calculations needed in model....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 477f33f6..6f05391a 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -202,97 +202,116 @@ SUBROUTINE canopy_calcs
                                     .and. cluref .gt. 0.0_rk) then
                                     !ISOP
                                     call canopy_bio(zk, fafraczInt, hcmref, &
-                                        lairef, cluref, cszref, dswrfref, tmp2mref, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         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, &
+                                        lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                        tleaf_ave, &
                                         lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                         19, emi_ovoc_3d(i,j,:))
                                 end if
@@ -481,97 +500,116 @@ SUBROUTINE canopy_calcs
                                 .and. cluref .gt. 0.0_rk) then
                                 !ISOP
                                 call canopy_bio(zk, fafraczInt, hcmref, &
-                                    lairef, cluref, cszref, dswrfref, tmp2mref, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     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, &
+                                    lairef, fsun, ppfd_sun, ppfd_shade, tleaf_sun, tleaf_shade, &
+                                    tleaf_ave, &
                                     lu_opt, vtyperef, modres, bio_cce, biovert_opt, co2_opt, co2_set, &
                                     19, emi_ovoc(loc,:))
                             end if

From 421855e50d0e444128c351db2f8230bd14ad5e1e Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 21 Jul 2023 16:16:23 -0400
Subject: [PATCH 55/64] Cleaned up bioemi code.

---
 src/canopy_bioemi_mod.F90 | 200 +-------------------------------------
 1 file changed, 1 insertion(+), 199 deletions(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index 228164ab..dfae2419 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -10,17 +10,13 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
         EMI_IND, EMI_OUT)
 
-!    SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, CLU, COSZEN, SFCRAD, &
-!        TEMP2, LU_OPT, VTYPE, MODRES, CCE, VERT, CO2OPT, CO2SET, &
-!        EMI_IND, EMI_OUT)
-
 !-----------------------------------------------------------------------
 
 ! Description:
 !     computes parameterized canopy biogenic emissions
 
 ! Preconditions:
-!     in-canopy FCLAI, model LAI, surface/skin temperature.
+!     in-canopy FCLAI, model LAI, etc.
 
 ! Subroutines and Functions Called:
 
@@ -49,7 +45,6 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         REAL(RK),    INTENT( IN )       :: ZK(:)           ! Model heights (m)
         REAL(RK),    INTENT( IN )       :: FCLAI(:)        ! Fractional (z) shapes of the
         ! plant surface distribution (nondimensional), i.e., a Fractional Culmulative LAI
-!add....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE, PPFD_SUN, PPFD_SHADE
         REAL(RK),    INTENT( IN )       :: FCH             ! Ccanopy height (m)
         REAL(RK),    INTENT( IN )       :: LAI             ! Total Leaf Area Index
         REAL(RK),    INTENT( IN )       :: FSUN(:)         ! Sunlit/Shaded fraction from photolysis correction factor
@@ -58,14 +53,6 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         REAL(RK),    INTENT( IN )       :: TLEAF_SUN(:)    ! Leaf temp for sunlit leaves (K)
         REAL(RK),    INTENT( IN )       :: TLEAF_SHADE(:)  ! Leaf temp for shaded leaves (K)
         REAL(RK),    INTENT( IN )       :: TLEAF_AVE(:)    ! Average Leaf temp (K)
-
-
-!---------comment out
-!        REAL(RK),    INTENT( IN )       :: CLU             ! Model input Clumping Index
-!        REAL(RK),    INTENT( IN )       :: COSZEN          ! Model input Cosine Solar Zenith Angle
-!        REAL(RK),    INTENT( IN )       :: SFCRAD          ! Model input Instantaneous surface downward shortwave flux (W/m2)
-!        REAL(RK),    INTENT( IN )       :: TEMP2           ! Model input 2-m Temperature (K)
-!---------
         INTEGER,     INTENT( IN )       :: LU_OPT          ! integer for LU type from model mapped to Massman et al. (default = 0/VIIRS)
         INTEGER,     INTENT( IN )       :: VTYPE           ! Grid cell dominant vegetation type
         REAL(RK),    INTENT( IN )       :: MODRES          ! Canopy model input vertical resolution (m)
@@ -77,22 +64,6 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         REAL(RK),    INTENT( OUT )      :: EMI_OUT(:)      ! Output canopy layer volume emissions (kg m-3 s-1)
 
 ! Local Variables
-!---------comment out
-!        REAL(RK) :: FSUN(SIZE(ZK))                 ! Sunlit/Shaded fraction from photolysis correction factor
-!        REAL(RK) :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
-!        REAL(RK) :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
-!        REAL(RK) :: ATEMP_SUN(SIZE(ZK))            ! Regression coefficient A for sun leaves (Silva et al., 2020)
-!        REAL(RK) :: BTEMP_SUN(SIZE(ZK))            ! Regression coefficient B for sun leaves
-!        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
-!        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
-!        REAL(RK) :: ATEMP_SHADE(SIZE(ZK))          ! Regression coefficient A for shade leaves
-!        REAL(RK) :: BTEMP_SHADE(SIZE(ZK))          ! Regression coefficient B for shade leaves
-!        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
-!        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
-!        REAL(RK) :: TLEAF_SUN(SIZE(ZK))            ! Leaf temp for sunlit leaves (K)
-!        REAL(RK) :: TLEAF_SHADE(SIZE(ZK))          ! Leaf temp for shaded leaves (K)
-!        REAL(RK) :: TLEAF_AVE(SIZE(ZK))            ! Average Leaf temp (K)
-!-------------
         REAL(RK) :: TLEAF24_AVE(SIZE(ZK))          ! Average Leaf temp over the past 24 hours (K)
         REAL(RK) :: TLEAF240_AVE(SIZE(ZK))         ! Average Leaf temp over the past 240 hours (K)
         REAL(RK) :: GammaTLEAF_SUN_NUM(SIZE(ZK))   ! Numerator in Tleaf sun activity factor
@@ -128,177 +99,8 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
         REAL(RK),          PARAMETER     :: PPFD0_SUN       =  200.0      !Constant PPFDo sunlit (umol/m2 s) (Guenther et al.,2012)
         REAL(RK),          PARAMETER     :: PPFD0_SHADE     =  50.0       !Constant PPFDo shaded (umol/m2 s) (Guenther et al.,2012)
-
-!----------------comment out
-!        REAL(RK),          PARAMETER     :: ATEMP_1_SUN     =  -13.891_rk !Linearized 2-m temp --> leaf temp parameters (Level 1 =
-!        !top of canopy
-!        REAL(RK),          PARAMETER     :: ATEMP_2_SUN     =  -12.322_rk !Based on Table 1 in Silva et al. (2022)
-!        REAL(RK),          PARAMETER     :: ATEMP_3_SUN     =  -1.032_rk  !
-!        REAL(RK),          PARAMETER     :: ATEMP_4_SUN     =  -5.172_rk  !
-!        REAL(RK),          PARAMETER     :: ATEMP_5_SUN     =  -5.589_rk  !...
-!        REAL(RK),          PARAMETER     :: BTEMP_1_SUN     =  1.064_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_2_SUN     =  1.057_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_3_SUN     =  1.031_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_4_SUN     =  1.050_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_5_SUN     =  1.051_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
-!        !top of canopy
-!        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
-!        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
-!        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
-!        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
-!        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
-!        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
-!        REAL(RK),          PARAMETER     :: ATEMP_1_SHADE   =  -12.846_rk !...
-!        REAL(RK),          PARAMETER     :: ATEMP_2_SHADE   =  -11.343_rk !...
-!        REAL(RK),          PARAMETER     :: ATEMP_3_SHADE   =  -1.068_rk  !...
-!        REAL(RK),          PARAMETER     :: ATEMP_4_SHADE   =  -5.551_rk  !...
-!        REAL(RK),          PARAMETER     :: ATEMP_5_SHADE   =  -5.955_rk  !...
-!        REAL(RK),          PARAMETER     :: BTEMP_1_SHADE   =  1.060_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_2_SHADE   =  1.053_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_3_SHADE   =  1.031_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_4_SHADE   =  1.051_rk   !...
-!        REAL(RK),          PARAMETER     :: BTEMP_5_SHADE   =  1.053_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
-!        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
-!        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
-!        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
-!        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
-!------------
-
-
         REAL(RK),          PARAMETER     :: CT2             =  230.0_rk   !Deactivation energy (kJ/mol) (Guenther et al., 2012)
 
-
-!------------comment out
-!!Calculate photolyis shading/correction factor through canopy, i.e., the fraction of sunlit leaves downward through canopy
-!!  `canopy_phot` gives relative direct beam irradiance,
-!!  which, multiplied by clumping index, gives sunlit fraction (e.g., Bonan 2019, eq. 14.18)
-!
-!        call canopy_phot(FCLAI, LAI, CLU, COSZEN, FSUN)
-!        FSUN = FSUN * CLU
-!
-!! Use linear canopy temperature model based on Silva et al. (2020) to get approx. sun/shade leaf temperatures
-!! through canopy (ignores effect of wind speed on leaf boundary layer ~ 1 % error/bias)
-!!Citation:
-!!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
-!!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
-!!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
-!        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
-!            if (ZK(i) .gt. FCH) then ! above canopy, Tleaf = Tair
-!                ATEMP_SUN(i)   = 0.0
-!                BTEMP_SUN(i)   = 1.0
-!                ATEMP_SHADE(i) = 0.0
-!                BTEMP_SHADE(i) = 1.0
-!            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
-!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ ATEMP_2_SUN,ATEMP_1_SUN /),ZK(i))
-!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ BTEMP_2_SUN,BTEMP_1_SUN /),ZK(i))
-!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ ATEMP_2_SHADE,ATEMP_1_SHADE /),ZK(i))
-!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ BTEMP_2_SHADE,BTEMP_1_SHADE /),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
-!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_3_SUN,ATEMP_2_SUN /),ZK(i))
-!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_3_SUN,BTEMP_2_SUN /),ZK(i))
-!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_3_SHADE,ATEMP_2_SHADE /),ZK(i))
-!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_3_SHADE,BTEMP_2_SHADE /),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
-!                ATEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_4_SUN,ATEMP_3_SUN /),ZK(i))
-!                BTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_4_SUN,BTEMP_3_SUN /),ZK(i))
-!                ATEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_4_SHADE,ATEMP_3_SHADE /),ZK(i))
-!                BTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_4_SHADE,BTEMP_3_SHADE /),ZK(i))
-!            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
-!                ATEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_5_SUN,ATEMP_4_SUN /),ZK(i))
-!                BTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_5_SUN,BTEMP_4_SUN /),ZK(i))
-!                ATEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ ATEMP_5_SHADE,ATEMP_4_SHADE /),ZK(i))
-!                BTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ BTEMP_5_SHADE,BTEMP_4_SHADE /),ZK(i))
-!            end if
-!        end do
-!
-!        TLEAF_SUN   = ATEMP_SUN + (BTEMP_SUN*TEMP2)
-!        TLEAF_SHADE = ATEMP_SHADE + (BTEMP_SHADE*TEMP2)
-!        TLEAF_AVE = (TLEAF_SUN*FSUN) + (TLEAF_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
-!
-!! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
-!! through canopy
-!!Citation:
-!!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
-!!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
-!!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
-!        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
-!            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
-!                CTEMP_SUN(i)   = 0.0
-!                DTEMP_SUN(i)   = 0.0
-!                CTEMP_SHADE(i) = 0.0
-!                DTEMP_SHADE(i) = 0.0
-!            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
-!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
-!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
-!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
-!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-!                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
-!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
-!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
-!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
-!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
-!                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
-!                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
-!                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
-!                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
-!            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
-!                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
-!                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
-!                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
-!                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-!                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
-!            end if
-!        end do
-!
-!        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
-!        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
-!----------------
-
-!Start here for biogenic calculations needed in model....new inputs FSUN, TLEAF_SUN, TLEAF_SHADE, TLEAF_AVE
-        !PPFD_SUN, PPFD_SHADE
-
 ! Calculate maximum normalized emission capacity (E_OPT) and Tleaf at E_OPT
         TLEAF240_AVE   = TLEAF_AVE  !Assume instantaneous TLEAF estimate for TLEAF240 and TLEAF24 (could improve...)
         TLEAF24_AVE    = TLEAF_AVE

From 3a0197aebe9343c2023d7bd211fe87610c7ee972 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Mon, 24 Jul 2023 14:47:21 -0400
Subject: [PATCH 56/64] Removed use canopy_phot_mod from bioemi.

---
 src/canopy_bioemi_mod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index dfae2419..87719db8 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -37,7 +37,6 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
 !-----------------------------------------------------------------------
         use canopy_const_mod, ONLY: rk,rgasuniv   !constants for canopy models
         use canopy_utils_mod,  ONLY: interp_linear1_internal, GET_GAMMA_CO2
-        use canopy_phot_mod
         use canopy_bioparm_mod
 
 ! Arguments:

From 6cf54290278560800d5ff6c98c534477727e3ad2 Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 28 Jul 2023 10:41:26 -0400
Subject: [PATCH 57/64] 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 87719db8..a67abd20 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -44,7 +44,7 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         REAL(RK),    INTENT( IN )       :: ZK(:)           ! Model heights (m)
         REAL(RK),    INTENT( IN )       :: FCLAI(:)        ! Fractional (z) shapes of the
         ! plant surface distribution (nondimensional), i.e., a Fractional Culmulative LAI
-        REAL(RK),    INTENT( IN )       :: FCH             ! Ccanopy height (m)
+        REAL(RK),    INTENT( IN )       :: FCH             ! Canopy height (m)
         REAL(RK),    INTENT( IN )       :: LAI             ! Total Leaf Area Index
         REAL(RK),    INTENT( IN )       :: FSUN(:)         ! Sunlit/Shaded fraction from photolysis correction factor
         REAL(RK),    INTENT( IN )       :: PPFD_SUN(:)     ! PPFD for sunlit leaves (umol phot/m2 s)

From 3f629d3e27f467b5d343d3c4facb5da79c39a8fd Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 28 Jul 2023 10:41:38 -0400
Subject: [PATCH 58/64] Update src/canopy_calcs.F90

Co-authored-by: Zachary Moon <zachary.moon@noaa.gov>
---
 src/canopy_calcs.F90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 6f05391a..7e3ce718 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -16,8 +16,8 @@ SUBROUTINE canopy_calcs
     use canopy_dxcalc_mod     !main canopy dx calculation
     use canopy_profile_mod    !main canopy foliage profile routines
     use canopy_rad_mod        !main canopy radiation sunlit/shaded routines
-    use canopy_tleaf_mod      !main canopy leaf temperature optons
-    use canopy_ppfd_mod       !main canopy leaf PPFD optons
+    use canopy_tleaf_mod      !main canopy leaf temperature options
+    use canopy_ppfd_mod       !main canopy leaf PPFD options
     use canopy_wind_mod       !main canopy components
     use canopy_waf_mod
     use canopy_phot_mod

From d7042a861e19b8cef261b3f88f40704a1fb1fe6e Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 28 Jul 2023 10:44:47 -0400
Subject: [PATCH 59/64] Removed uneeded FRAC_PAR from bioemi.

---
 src/canopy_bioemi_mod.F90 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/canopy_bioemi_mod.F90 b/src/canopy_bioemi_mod.F90
index a67abd20..16d618ba 100644
--- a/src/canopy_bioemi_mod.F90
+++ b/src/canopy_bioemi_mod.F90
@@ -95,7 +95,6 @@ SUBROUTINE CANOPY_BIO( ZK, FCLAI, FCH, LAI, FSUN, PPFD_SUN, &
         integer i, LAYERS
 
 ! Constant Canopy Parameters
-        REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
         REAL(RK),          PARAMETER     :: PPFD0_SUN       =  200.0      !Constant PPFDo sunlit (umol/m2 s) (Guenther et al.,2012)
         REAL(RK),          PARAMETER     :: PPFD0_SHADE     =  50.0       !Constant PPFDo shaded (umol/m2 s) (Guenther et al.,2012)
         REAL(RK),          PARAMETER     :: CT2             =  230.0_rk   !Deactivation energy (kJ/mol) (Guenther et al., 2012)

From 3816304ba83d9c18a92f6c0a80ea022b8688549d Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 28 Jul 2023 10:57:45 -0400
Subject: [PATCH 60/64] Removed ppfd_mod and combined into rad_mod

---
 src/Makefile            |   1 -
 src/canopy_calcs.F90    |   3 +-
 src/canopy_ppfd_mod.F90 | 130 ----------------------------------------
 src/canopy_rad_mod.F90  | 123 +++++++++++++++++++++++++++++++++++++
 4 files changed, 124 insertions(+), 133 deletions(-)
 delete mode 100644 src/canopy_ppfd_mod.F90

diff --git a/src/Makefile b/src/Makefile
index 0ffe4008..41bf8b0d 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -69,7 +69,6 @@ OBJS :=\
  canopy_profile_mod.o \
  canopy_phot_mod.o \
  canopy_rad_mod.o \
- canopy_ppfd_mod.o \
  canopy_tleaf_mod.o \
  canopy_wind_mod.o \
  canopy_waf_mod.o \
diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 7e3ce718..68214e80 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -16,8 +16,7 @@ SUBROUTINE canopy_calcs
     use canopy_dxcalc_mod     !main canopy dx calculation
     use canopy_profile_mod    !main canopy foliage profile routines
     use canopy_rad_mod        !main canopy radiation sunlit/shaded routines
-    use canopy_tleaf_mod      !main canopy leaf temperature options
-    use canopy_ppfd_mod       !main canopy leaf PPFD options
+    use canopy_tleaf_mod      !main canopy leaf temperature sunlit/shaded routines
     use canopy_wind_mod       !main canopy components
     use canopy_waf_mod
     use canopy_phot_mod
diff --git a/src/canopy_ppfd_mod.F90 b/src/canopy_ppfd_mod.F90
deleted file mode 100644
index 37582b9f..00000000
--- a/src/canopy_ppfd_mod.F90
+++ /dev/null
@@ -1,130 +0,0 @@
-module canopy_ppfd_mod
-
-    implicit none
-
-contains
-
-!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-    SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, FSUN, &
-        PPFD_SUN, PPFD_SHADE, PPFD_AVE)
-
-!-----------------------------------------------------------------------
-
-! Description:
-!     computes linear interpolation method for PPFD sun/shade in canopy.
-
-! Preconditions:
-!     in-canopy height, and model LAI, clumping index, and solar zenith angle
-
-! Subroutines and Functions Called:
-
-! Revision History:
-!     Prototype 06/23 by PCC
-!     Jun 2023 P.C. Campbell: Initial standalone PPFD linear subroutine based on
-!                             Silva et al. (2020) exponential curve algorithms
-!-----------------------------------------------------------------------
-!-----------------------------------------------------------------------
-        use canopy_const_mod, ONLY: RK     !constants for canopy models
-        use canopy_utils_mod,  ONLY: interp_linear1_internal
-
-! Arguments:
-!     IN/OUT
-        REAL(RK),    INTENT( IN )       :: ZK(:)                          ! Input model heights (m)
-        REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
-        REAL(RK),    INTENT( IN )       :: SFCRAD                         ! Model input Instantaneous surface downward shortwave flux (W/m2)
-        REAL(RK),    INTENT( IN )       :: LAI                            ! Model input total Leaf Area Index
-        REAL(RK),    INTENT( IN )       :: FSUN(:)                        ! Sunlit/Shaded fraction from photolysis correction factor
-        REAL(RK),    INTENT( OUT )      :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
-        REAL(RK),    INTENT( OUT )      :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
-        REAL(RK),    INTENT( OUT )      :: PPFD_AVE(SIZE(ZK))             ! Average PPFD for sunlit and shaded leaves (umol phot/m2 s)
-
-!      LOCAL
-        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
-        !top of canopy
-        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
-        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
-        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
-        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
-        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
-        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
-        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
-        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
-
-        REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
-
-        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
-        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
-        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
-        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
-
-        integer i
-
-! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
-! through canopy
-!Citation:
-!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
-!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
-!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
-        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
-            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
-                CTEMP_SUN(i)   = 0.0
-                DTEMP_SUN(i)   = 0.0
-                CTEMP_SHADE(i) = 0.0
-                DTEMP_SHADE(i) = 0.0
-            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
-                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
-                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
-                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
-                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
-            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
-                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
-                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
-                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
-                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
-                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
-            end if
-        end do
-
-        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
-        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
-        PPFD_AVE = (PPFD_SUN*FSUN) + (PPFD_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
-
-    END SUBROUTINE CANOPY_PPFD_EXP
-
-end module canopy_ppfd_mod
diff --git a/src/canopy_rad_mod.F90 b/src/canopy_rad_mod.F90
index 579cc183..163f7a5c 100644
--- a/src/canopy_rad_mod.F90
+++ b/src/canopy_rad_mod.F90
@@ -44,4 +44,127 @@ SUBROUTINE CANOPY_FSUN_CLU( FCLAI, LAI, CLU, COSZEN, FSUN)
 
     END SUBROUTINE CANOPY_FSUN_CLU
 
+!:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+    SUBROUTINE CANOPY_PPFD_EXP( ZK, FCH, SFCRAD, LAI, FSUN, &
+        PPFD_SUN, PPFD_SHADE, PPFD_AVE)
+
+!-----------------------------------------------------------------------
+
+! Description:
+!     computes linear interpolation method for PPFD sun/shade in canopy.
+
+! Preconditions:
+!     in-canopy height, and model LAI, clumping index, and solar zenith angle
+
+! Subroutines and Functions Called:
+
+! Revision History:
+!     Prototype 06/23 by PCC
+!     Jun 2023 P.C. Campbell: Initial standalone PPFD linear subroutine based on
+!                             Silva et al. (2020) exponential curve algorithms
+!-----------------------------------------------------------------------
+!-----------------------------------------------------------------------
+        use canopy_const_mod, ONLY: RK     !constants for canopy models
+        use canopy_utils_mod,  ONLY: interp_linear1_internal
+
+! Arguments:
+!     IN/OUT
+        REAL(RK),    INTENT( IN )       :: ZK(:)                          ! Input model heights (m)
+        REAL(RK),    INTENT( IN )       :: FCH                            ! Model input canopy height (m)
+        REAL(RK),    INTENT( IN )       :: SFCRAD                         ! Model input Instantaneous surface downward shortwave flux (W/m2)
+        REAL(RK),    INTENT( IN )       :: LAI                            ! Model input total Leaf Area Index
+        REAL(RK),    INTENT( IN )       :: FSUN(:)                        ! Sunlit/Shaded fraction from photolysis correction factor
+        REAL(RK),    INTENT( OUT )      :: PPFD_SUN(SIZE(ZK))             ! PPFD for sunlit leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( OUT )      :: PPFD_SHADE(SIZE(ZK))           ! PPFD for shaded leaves (umol phot/m2 s)
+        REAL(RK),    INTENT( OUT )      :: PPFD_AVE(SIZE(ZK))             ! Average PPFD for sunlit and shaded leaves (umol phot/m2 s)
+
+!      LOCAL
+        REAL(RK),          PARAMETER     :: CTEMP_1_SUN     =  1.083_rk   !Exponential 2-m PPFD --> PPFD parameters (Level 1 =
+        !top of canopy
+        REAL(RK),          PARAMETER     :: CTEMP_2_SUN     =  1.096_rk   !Based on Table 1 in Silva et al. (2022)
+        REAL(RK),          PARAMETER     :: CTEMP_3_SUN     =  1.104_rk   !
+        REAL(RK),          PARAMETER     :: CTEMP_4_SUN     =  1.098_rk   !
+        REAL(RK),          PARAMETER     :: CTEMP_5_SUN     =  1.090_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_1_SUN     =  0.002_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_2_SUN     =  -0.128_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_3_SUN     =  -0.298_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_4_SUN     =  -0.445_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_5_SUN     =  -0.535_rk  !...
+        REAL(RK),          PARAMETER     :: CTEMP_1_SHADE   =  0.871_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_2_SHADE   =  0.890_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_3_SHADE   =  0.916_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_4_SHADE   =  0.941_rk   !...
+        REAL(RK),          PARAMETER     :: CTEMP_5_SHADE   =  0.956_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_1_SHADE   =  0.015_rk   !...
+        REAL(RK),          PARAMETER     :: DTEMP_2_SHADE   =  -0.141_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_3_SHADE   =  -0.368_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_4_SHADE   =  -0.592_rk  !...
+        REAL(RK),          PARAMETER     :: DTEMP_5_SHADE   =  -0.743_rk  !...
+
+        REAL(RK),          PARAMETER     :: FRAC_PAR        =  0.5_rk     !Fraction of incoming solar irradiance that is PAR
+
+        REAL(RK) :: CTEMP_SUN(SIZE(ZK))            ! Regression coefficient C for sun leaves
+        REAL(RK) :: DTEMP_SUN(SIZE(ZK))            ! Regression coefficient D for sun leaves
+        REAL(RK) :: CTEMP_SHADE(SIZE(ZK))          ! Regression coefficient C for shade leaves
+        REAL(RK) :: DTEMP_SHADE(SIZE(ZK))          ! Regression coefficient D for shade leaves
+
+        integer i
+
+! Use exponential PPFD model based on Silva et al. (2020) to get approx. sun/shade PPFD
+! through canopy
+!Citation:
+!Silva, S. J., Heald, C. L., and Guenther, A. B.: Development of a reduced-complexity plant canopy
+!physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0,
+!Geosci. Model Dev., 13, 2569–2585, https://doi.org/10.5194/gmd-13-2569-2020, 2020.
+        do i=1, SIZE(ZK)  !calculate linear change in parameters interpolated to Silva et al. 5 layer canopy regions
+            if (ZK(i) .gt. FCH) then ! above canopy, PPFD_leaf = PPFD_toc (toc=top of canopy)
+                CTEMP_SUN(i)   = 0.0
+                DTEMP_SUN(i)   = 0.0
+                CTEMP_SHADE(i) = 0.0
+                DTEMP_SHADE(i) = 0.0
+            else if (ZK(i) .le. FCH .and. ZK(i) .gt. FCH*(4.0_rk/5.0_rk)) then  !Level 1 - 2
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ CTEMP_2_SUN,CTEMP_1_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ DTEMP_2_SUN,DTEMP_1_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ CTEMP_2_SHADE,CTEMP_1_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(4.0_rk/5.0_rk),FCH /), &
+                    (/ DTEMP_2_SHADE,DTEMP_1_SHADE /),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
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ CTEMP_3_SUN,CTEMP_2_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ DTEMP_3_SUN,DTEMP_2_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ CTEMP_3_SHADE,CTEMP_2_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(3.0_rk/5.0_rk),FCH*(4.0_rk/5.0_rk) /), &
+                    (/ DTEMP_3_SHADE,DTEMP_2_SHADE /),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
+                CTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ CTEMP_4_SUN,CTEMP_3_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ DTEMP_4_SUN,DTEMP_3_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ CTEMP_4_SHADE,CTEMP_3_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ FCH*(2.0_rk/5.0_rk),FCH*(3.0_rk/5.0_rk) /), &
+                    (/ DTEMP_4_SHADE,DTEMP_3_SHADE /),ZK(i))
+            else if (ZK(i) .le. FCH*(2.0_rk/5.0_rk) ) then  !Level 4 - Bottom
+                CTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ CTEMP_5_SUN,CTEMP_4_SUN /),ZK(i))
+                DTEMP_SUN(i)   = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ DTEMP_5_SUN,DTEMP_4_SUN /),ZK(i))
+                CTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ CTEMP_5_SHADE,CTEMP_4_SHADE /),ZK(i))
+                DTEMP_SHADE(i) = interp_linear1_internal((/ ZK(1),FCH*(2.0_rk/5.0_rk) /), &
+                    (/ DTEMP_5_SHADE,DTEMP_4_SHADE /),ZK(i))
+            end if
+        end do
+
+        PPFD_SUN     = FRAC_PAR * SFCRAD * EXP(CTEMP_SUN + DTEMP_SUN * LAI)  !Silva et al. W/m2 --> umol m-2 s-1
+        PPFD_SHADE   = FRAC_PAR * SFCRAD * EXP(CTEMP_SHADE + DTEMP_SHADE * LAI)
+        PPFD_AVE = (PPFD_SUN*FSUN) + (PPFD_SHADE*(1.0-FSUN)) ! average = sum sun and shade weighted by sunlit fraction
+
+    END SUBROUTINE CANOPY_PPFD_EXP
+
 end module canopy_rad_mod

From 4fcce8a7e87f723514e2751d61f483124c9d2d63 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 28 Jul 2023 16:15:47 -0400
Subject: [PATCH 61/64] Fix/Update conditions on flameh and WAF calculations.

---
 src/canopy_calcs.F90 | 52 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/canopy_calcs.F90 b/src/canopy_calcs.F90
index 68214e80..5ced80cd 100644
--- a/src/canopy_calcs.F90
+++ b/src/canopy_calcs.F90
@@ -171,12 +171,26 @@ SUBROUTINE canopy_calcs
 ! ... determine midflamepoint and flame height from user or FRP calculation
                                 call canopy_flameh(flameh_opt, flameh_set, dx_2d(i,j), modres, &
                                     frpref, frp_fac, hcmref, midflamepoint, flameh_2d(i,j))
-
-                                if (flameh_2d(i,j) .gt. 0.0 .and. flameh_2d(i,j) .le. hcmref) then
-                                    !only calculate WAF when flameh > 0 and <= FH
-                                    call canopy_waf(hcmref, lambdars, hgtref, flameh_2d(i,j), &
-                                        firetype, d_h, zo_h, canBOT(midflamepoint), &
-                                        canTOP(midflamepoint), waf_2d(i,j))
+                                if (firetype .eq. 0) then !forest/sub-canopy firetype
+                                    if (flameh_2d(i,j) .gt. 0.0) then !flameh must be > 0
+                                        if (flameh_2d(i,j) .le. hcmref) then !only calculate when flameh <= FCH
+                                            call canopy_waf(hcmref, lambdars, hgtref, flameh_2d(i,j), &
+                                                firetype, d_h, zo_h, canBOT(midflamepoint), &
+                                                canTOP(midflamepoint), waf_2d(i,j))
+                                        else
+                                            write(*,*) 'warning...sub-canopy type fire, but flameh > FCH, setting WAF=1'
+                                            waf_2d(i,j) = 1.0_rk
+                                        end if
+                                    end if
+                                else  !grass/crops, above-canopy firetype
+                                    if (flameh_2d(i,j) .gt. 0.0) then !flameh still must be > 0
+                                        call canopy_waf(hcmref, lambdars, hgtref, flameh_2d(i,j), &
+                                            firetype, d_h, zo_h, canBOT(midflamepoint), &
+                                            canTOP(midflamepoint), waf_2d(i,j))
+                                    end if
+                                end if
+                                if (waf_2d(i,j) .gt. 1.0_rk) then !Final check of WAF > 1, must be <=1
+                                    waf_2d(i,j) = 1.0_rk
                                 end if
                             end if
 
@@ -469,12 +483,26 @@ SUBROUTINE canopy_calcs
 ! ... determine midflamepoint and flame height from user or FRP calculation
                             call canopy_flameh(flameh_opt, flameh_set, dx(loc), modres, &
                                 frpref, frp_fac, hcmref, midflamepoint, flameh(loc))
-
-                            if (flameh(loc) .gt. 0.0 .and. flameh(loc) .le. hcmref) then
-                                !only calculate WAF when flameh > 0
-                                call canopy_waf(hcmref, lambdars, hgtref, flameh(loc), &
-                                    firetype, d_h, zo_h, canBOT(midflamepoint), &
-                                    canTOP(midflamepoint), waf(loc))
+                            if (firetype .eq. 0) then !forest/sub-canopy firetype
+                                if (flameh(loc) .gt. 0.0) then !flameh must be > 0
+                                    if (flameh(loc) .le. hcmref) then !only calculate when flameh <= FCH
+                                        call canopy_waf(hcmref, lambdars, hgtref, flameh(loc), &
+                                            firetype, d_h, zo_h, canBOT(midflamepoint), &
+                                            canTOP(midflamepoint), waf(loc))
+                                    else
+                                        write(*,*) 'warning...sub-canopy type fire, but flameh > FCH, setting WAF=1'
+                                        waf(loc) = 1.0_rk
+                                    end if
+                                end if
+                            else  !grass/crops, above-canopy firetype
+                                if (flameh(loc) .gt. 0.0) then !flameh still must be > 0
+                                    call canopy_waf(hcmref, lambdars, hgtref, flameh(loc), &
+                                        firetype, d_h, zo_h, canBOT(midflamepoint), &
+                                        canTOP(midflamepoint), waf(loc))
+                                end if
+                            end if
+                            if (waf(loc) .gt. 1.0_rk) then !Final check of WAF > 1, must be <=1
+                                waf(loc) = 1.0_rk
                             end if
                         end if
 

From 6465d05a7635cab256598cd73e47c940d7248245 Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 4 Aug 2023 15:51:56 -0400
Subject: [PATCH 62/64] Update python/README.md

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

diff --git a/python/README.md b/python/README.md
index 447ab8df..c7dfe85d 100644
--- a/python/README.md
+++ b/python/README.md
@@ -78,7 +78,7 @@ You can also download and generate global gridded canopy-app inputs using Python
    conda activate canopy-app
    ```
 
-3. Run python script
+3. Run Python script
 
    ```
    python global_data_process.py

From d7cfa3a139f06728748e1c0d0dac9e651cde5835 Mon Sep 17 00:00:00 2001
From: drnimbusrain <dr.nimbusrain@gmail.com>
Date: Fri, 4 Aug 2023 15:58:17 -0400
Subject: [PATCH 63/64] Fixing gfortran debug check for CI case.

---
 src/Makefile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index 41bf8b0d..681d98d6 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -19,7 +19,7 @@ NC ?= 1
 # Compile flags
 $(info DEBUG setting: '$(DEBUG)')
 ifeq ($(DEBUG), 1)
-  ifeq ($(FC),gfortran)
+  ifeq ($(findstring gfortran,$(notdir $(FC))),gfortran)
     FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5 -std=f2003 -fall-intrinsics
   else ifeq ($(FC),ifort)
     FCFLAGS := -g -warn all -check bounds -implicitnone -O0 -error-limit 5
@@ -29,6 +29,7 @@ else ifeq ($(DEBUG), 0)
 else
   $(error invalid setting for DEBUG, should be 0 or 1 but is '$(DEBUG)')
 endif
+$(info FCFLAGS: '$(FCFLAGS)')
 
 # NETCDF Settings here
 LIBS :=

From 73334b8d6a78249bf3f63ca260415b1222bf02dd Mon Sep 17 00:00:00 2001
From: Patrick Campbell <dr.nimbusrain@gmail.com>
Date: Fri, 4 Aug 2023 21:46:41 -0400
Subject: [PATCH 64/64] 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 ec710c8c..92388d32 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ See [the included Makefile](./src/Makefile), which detects NetCDF using `nf-conf
 
 Compilation options can be controlled with environment variables:
 
-- `FC=gfortran` (default) or ifort
+- `FC=gfortran` (default) or compiler name/path (e.g. `FC=ifort`, `FC=gfortran-11`, `FC=/usr/bin/gfortran-11`)
 - `DEBUG=0` (off; default) or `DEBUG=1` (on)
 - `NC=0` (off) or `NC=1` (on; default)