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Bio opts #73

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merged 25 commits into from
Jun 12, 2023
Merged

Bio opts #73

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a0806e1
Initial commit for new biogenic related options.
drnimbusrain May 19, 2023
570037a
Forced bio_vert option to only default =0 right now...
drnimbusrain May 20, 2023
cf5275f
Added new bio_vert=1 option for MEGANv3-like sum.
drnimbusrain May 22, 2023
abbe51b
Added new crop_opt to specify crop type heights.
drnimbusrain May 23, 2023
1735957
Updated README
drnimbusrain May 23, 2023
e43d32b
Added bio_vert=2 option for LAD weighted sum.
drnimbusrain May 23, 2023
2df0184
Switched bio_vert option 1 and 2.
drnimbusrain May 24, 2023
e229622
Added new gaussian bio_vert option, and moved others around.
drnimbusrain May 25, 2023
949f011
Added new shrub/savanna/grass (SSG) user options (ssg_opt).
drnimbusrain May 25, 2023
2307fb9
Added new CO2 inhibition factor (co2_opt) for biogenic emissions.
drnimbusrain May 31, 2023
f12a839
Updated README.
drnimbusrain May 31, 2023
7060b6b
Updated README.
drnimbusrain May 31, 2023
e89dc13
Update README.md
drnimbusrain Jun 1, 2023
888eea2
Removed HEMCO header.
drnimbusrain Jun 1, 2023
38c59dd
Update src/canopy_bioemi_mod.F90
drnimbusrain Jun 2, 2023
1c6481f
Added LAYERS+1 for all bio_vert options for summing.
drnimbusrain Jun 2, 2023
a42c9a8
Updated README for co2_inhibition warning.
drnimbusrain Jun 2, 2023
fb6c4e7
Updated README for co2 inhibition note.
drnimbusrain Jun 4, 2023
4d43d2c
Add small example comparing the emissions calc opts
zmoon Jun 8, 2023
65993ea
Add missing emi calc option
zmoon Jun 8, 2023
c076b6f
Changed bio_vert to biovert_opt to conform NL.
drnimbusrain Jun 9, 2023
a100e9d
Merge branch 'bio_opts' of https://github.com/noaa-oar-arl/canopy-app…
drnimbusrain Jun 9, 2023
9d61034
Updated NL for biovert_opt = 0 by default
drnimbusrain Jun 9, 2023
d3e7420
Fixed README for biovert_opt.
drnimbusrain Jun 9, 2023
f851b4e
Update python/examples.ipynb
drnimbusrain Jun 10, 2023
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7 changes: 7 additions & 0 deletions README.md
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Expand Up @@ -197,6 +197,13 @@ 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 |
| `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`) |
| `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 |
| `fch_thresh` | user-set real value of canopy height threshold for contiguous canopy (m) |
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63 changes: 35 additions & 28 deletions input/namelist.canopy
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Expand Up @@ -5,32 +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
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 = 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
/
58 changes: 58 additions & 0 deletions python/examples.ipynb
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Expand Up @@ -760,6 +760,64 @@
" 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",
" biovert_opt=[0, 1, 2, 3],\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 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)."
]
},
{
"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",
"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)"
]
}
],
"metadata": {
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101 changes: 91 additions & 10 deletions src/canopy_bioemi_mod.F90
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Expand Up @@ -6,7 +6,8 @@ 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, CO2OPT, CO2SET, &
EMI_IND, EMI_OUT)

!-----------------------------------------------------------------------

Expand All @@ -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

Expand All @@ -51,6 +52,9 @@ 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 ) :: 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)

Expand Down Expand Up @@ -92,10 +96,13 @@ 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) :: 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)
integer i
REAL(RK) :: GAMMACO2 ! CO2 inhibition factor (isoprene only)
integer i, LAYERS

! Constant Canopy Parameters
REAL(RK), PARAMETER :: FRAC_PAR = 0.5_rk !Fraction of incoming solar irradiance that is PAR
Expand Down Expand Up @@ -298,15 +305,89 @@ 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

! 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
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)
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) * 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
else if (VERT .eq. 1) then !"MEGANv3-like": Use weighting factors normalized to plant distribution shape (FCLAI)
!across canopy layers
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)
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)) * 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
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!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) + 1
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)) * 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
!--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) + 1
do i=1, SIZE(ZK)
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)) * 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 BIOVERT_OPT choice of ', VERT, ' in namelist...exiting'
call exit(2)
end if

END SUBROUTINE CANOPY_BIO

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