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1. DECOMP_SCHEME = 2. Updated so it follows the CENTURY implementatio…
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…n by Bolker et al.

    (1998) more closely.  With this option the code enables 5 time-related pools
    (metabolic litter aka fast, structural, microbial, humified aka slow, and passive).
2.  For all DECOMP_SCHEME cases, now both the "fast" and "structural pools are split into
    above- and below-ground.  This is not because they have different typical decay rates,
    but because we need the above-ground fraction for the fire model both to account for
    fuels and to burn them.
3.  Minor bug fix to H2O_PLANT_LIM = 3.  When leaf is not resolved, stomatal conductance
    must be set to a non-zero value, to avoid singularities when the plant becomes active
    again.
4.  Updates to R scripts and Template directory, so the Template ED2IN no longer has
    paths that are specific to odyssey.
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mpaiao committed Aug 9, 2018
1 parent 73d08c7 commit 21344b5
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30 changes: 17 additions & 13 deletions BRAMS/Template/RAMSIN
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Original file line number Diff line number Diff line change
Expand Up @@ -2425,20 +2425,18 @@ $ED2_INFO


!---------------------------------------------------------------------------------------!
! DECOMP_SCHEME -- This specifies the dependence of soil decomposition on temperature. !
! 0. ED-2.1 default, the original exponential (low temperature !
! limitation only). !
! 1. Lloyd and Taylor (1994) model !
! DECOMP_SCHEME -- This specifies the soil Carbon (decomposition) model. !
! 0. ED-2.1 default, with three soil carbon pools. Temperature the !
! original exponential (low temperature limitation only). !
! 1. Similar to option 0, except that temperature is solved using !
! the Lloyd and Taylor (1994) model. !
! [[option 1 requires parameters to be set in xml]] !
! 2. RothC model, which contains one extra pools (microbial SOM), !
! based on Sierra et al. (2012, GMD). The inertial/passive pool !
! was not included because RothC assumes it to be completely !
! detached from the other ground/soil carbon pools. Thee temper- !
! ature and moisture dependencies are similar to ED-1.0 and the !
! CENTURY models, although the functional forms were rewritten so !
! the functions were continuous AND differentiable (moisture) and !
! without the risk of FPE due to the square root of negative !
! numbers (temperature). !
! 2. Based on Bolker et al. (1998) CENTURY model. Five necromass !
! pools (litter aka fast, structural, microbial, !
! humified aka slow, and passive). Temperature and moisture !
! functions are similar to Bolker et al. (1998) and ED-1.0, except !
! that the curves were refitted to make them continuous and !
! differentiable. !
!---------------------------------------------------------------------------------------!
DECOMP_SCHEME = 2,
!---------------------------------------------------------------------------------------!
Expand All @@ -2461,6 +2459,12 @@ $ED2_INFO
! where psi is the matric potentital at layer k, z is the layer !
! depth, H it the crown height and psi_fc and psi_wp are the !
! matric potentials at wilting point and field capacity. !
! 3. Similar to 2, but the water supply directly affects gsw, as !
! opposed to fsw. This is done by making D0 a function of soil !
! moisture, as means to avoid double counting the effect of VPD on !
! stomatal conductance. Note that this still uses Kw but Kw must !
! be significantly lower, at least for tropical trees (1/15 - 1/10 !
! of the original). !
!---------------------------------------------------------------------------------------!
H2O_PLANT_LIM = 2,
!---------------------------------------------------------------------------------------!
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30 changes: 17 additions & 13 deletions BRAMS/run/RAMSIN
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Original file line number Diff line number Diff line change
Expand Up @@ -2463,20 +2463,18 @@ $ED2_INFO


!---------------------------------------------------------------------------------------!
! DECOMP_SCHEME -- This specifies the dependence of soil decomposition on temperature. !
! 0. ED-2.1 default, the original exponential (low temperature !
! limitation only). !
! 1. Lloyd and Taylor (1994) model !
! DECOMP_SCHEME -- This specifies the soil Carbon (decomposition) model. !
! 0. ED-2.1 default, with three soil carbon pools. Temperature the !
! original exponential (low temperature limitation only). !
! 1. Similar to option 0, except that temperature is solved using !
! the Lloyd and Taylor (1994) model. !
! [[option 1 requires parameters to be set in xml]] !
! 2. RothC model, which contains one extra pools (microbial SOM), !
! based on Sierra et al. (2012, GMD). The inertial/passive pool !
! was not included because RothC assumes it to be completely !
! detached from the other ground/soil carbon pools. Thee temper- !
! ature and moisture dependencies are similar to ED-1.0 and the !
! CENTURY models, although the functional forms were rewritten so !
! the functions were continuous AND differentiable (moisture) and !
! without the risk of FPE due to the square root of negative !
! numbers (temperature). !
! 2. Based on Bolker et al. (1998) CENTURY model. Five necromass !
! pools (litter aka fast, structural, microbial, !
! humified aka slow, and passive). Temperature and moisture !
! functions are similar to Bolker et al. (1998) and ED-1.0, except !
! that the curves were refitted to make them continuous and !
! differentiable. !
!---------------------------------------------------------------------------------------!
DECOMP_SCHEME = 2,
!---------------------------------------------------------------------------------------!
Expand All @@ -2499,6 +2497,12 @@ $ED2_INFO
! where psi is the matric potentital at layer k, z is the layer !
! depth, H it the crown height and psi_fc and psi_wp are the !
! matric potentials at wilting point and field capacity. !
! 3. Similar to 2, but the water supply directly affects gsw, as !
! opposed to fsw. This is done by making D0 a function of soil !
! moisture, as means to avoid double counting the effect of VPD on !
! stomatal conductance. Note that this still uses Kw but Kw must !
! be significantly lower, at least for tropical trees (1/15 - 1/10 !
! of the original). !
!---------------------------------------------------------------------------------------!
H2O_PLANT_LIM = 2,
!---------------------------------------------------------------------------------------!
Expand Down
42 changes: 23 additions & 19 deletions ED/Template/Template/ED2IN
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Original file line number Diff line number Diff line change
Expand Up @@ -562,14 +562,14 @@ $ED_NL
! soil temperature and moisture. !
! SOILDEPTH_DB -- Dataset in case you want to read in soil depth information. !
!---------------------------------------------------------------------------------------!
NL%VEG_DATABASE = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/oge2OLD/OGE2_'
NL%SOIL_DATABASE = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/soil_ed22/Quesada+RADAM+IGBP/Quesada+RADAM+IGBP_'
NL%VEG_DATABASE = 'myinpmain/veget_data/OGE2/OGE2_'
NL%SOIL_DATABASE = 'myinpmain/soil_data/texture/Quesada+RADAM+IGBP/Quesada+RADAM+IGBP_'
NL%LU_DATABASE = 'myludatabase'
NL%PLANTATION_FILE = ''
NL%THSUMS_DATABASE = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/ed_inputs/'
NL%THSUMS_DATABASE = 'myinpmain/thermal_sums/'
NL%ED_MET_DRIVER_DB = 'mymetdriverdb'
NL%SOILSTATE_DB = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/ed_inputs/STW1996OCT.dat'
NL%SOILDEPTH_DB = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/ed_inputs/soil_depths.dat'
NL%SOILSTATE_DB = 'myinpmain/soil_data/temp+moist/STW1996OCT.dat'
NL%SOILDEPTH_DB = 'myinpmain/soil_data/depth/soil_depths.dat'
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -949,20 +949,18 @@ $ED_NL


!---------------------------------------------------------------------------------------!
! DECOMP_SCHEME -- This specifies the dependence of soil decomposition on temperature. !
! 0. ED-2.1 default, the original exponential (low temperature !
! limitation only). !
! 1. Lloyd and Taylor (1994) model !
! DECOMP_SCHEME -- This specifies the soil Carbon (decomposition) model. !
! 0. ED-2.1 default, with three soil carbon pools. Temperature the !
! original exponential (low temperature limitation only). !
! 1. Similar to option 0, except that temperature is solved using !
! the Lloyd and Taylor (1994) model. !
! [[option 1 requires parameters to be set in xml]] !
! 2. RothC model, which contains one extra pools (microbial SOM), !
! based on Sierra et al. (2012, GMD). The inertial/passive pool !
! was not included because RothC assumes it to be completely !
! detached from the other ground/soil carbon pools. Thee temper- !
! ature and moisture dependencies are similar to ED-1.0 and the !
! CENTURY models, although the functional forms were rewritten so !
! the functions were continuous AND differentiable (moisture) and !
! without the risk of FPE due to the square root of negative !
! numbers (temperature). !
! 2. Based on Bolker et al. (1998) CENTURY model. Five necromass !
! pools (litter aka fast, structural, microbial, !
! humified aka slow, and passive). Temperature and moisture !
! functions are similar to Bolker et al. (1998) and ED-1.0, except !
! that the curves were refitted to make them continuous and !
! differentiable. !
!---------------------------------------------------------------------------------------!
NL%DECOMP_SCHEME = mydecomp
!---------------------------------------------------------------------------------------!
Expand All @@ -986,6 +984,12 @@ $ED_NL
! where psi is the matric potentital at layer k, z is the layer !
! depth, H it the crown height and psi_fc and psi_wp are the !
! matric potentials at wilting point and field capacity. This is !
! 3. Similar to 2, but the water supply directly affects gsw, as !
! opposed to fsw. This is done by making D0 a function of soil !
! moisture, as means to avoid double counting the effect of VPD on !
! stomatal conductance. Note that this still uses Kw but Kw must !
! be significantly lower, at least for tropical trees (1/15 - 1/10 !
! of the original). !
!---------------------------------------------------------------------------------------!
NL%H2O_PLANT_LIM = myh2olimit
!---------------------------------------------------------------------------------------!
Expand Down Expand Up @@ -1599,7 +1603,7 @@ $ED_NL
NL%IPHENYSF = 2003
NL%IPHENYF1 = 1992
NL%IPHENYFF = 2003
NL%PHENPATH = '/n/gstore/Labs/moorcroft_lab_protected/data/ed2_data/phenology/phenology'
NL%PHENPATH = 'myinpdata/phenology/phenology'
!---------------------------------------------------------------------------------------!


Expand Down
37 changes: 24 additions & 13 deletions ED/Template/Template/plot_yearly.r
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Original file line number Diff line number Diff line change
Expand Up @@ -690,6 +690,9 @@ for (place in myplaces){
}#end if
#----- Check whether the user wants to have this variable plotted. ------------------#
if (plotit && length(pftuse) > 0 && any(is.finite(thisvar))){
#------ Append "all" to the PFT classes to plot. ---------------------------------#
pftplt = c(pftuse,npft+1)
#---------------------------------------------------------------------------------#

#---------------------------------------------------------------------------------#
# Check whether the time series directory exists. If not, create it. #
Expand All @@ -707,28 +710,36 @@ for (place in myplaces){
# Find the limit, make some room for the legend, and in case the field is a #
# constant, nudge the limits so the plot command will not complain. #
#---------------------------------------------------------------------------------#
xlimit = pretty.xylim(u=datum$toyear ,fracexp=0.0,is.log=FALSE)
ylimit = pretty.xylim(u=thisvar[,,pftuse],fracexp=0.0,is.log=plog)
if (plog){
xylog = "y"
ydrought = c( exp(sqrt(ylimit[1]^3/ylimit[2]))
, exp(sqrt(ylimit[2]^3/ylimit[1]))
)#end c
}else{
xylog = ""
ydrought = c( ylimit[1] - 0.5 * diff(ylimit),ylimit[2] + 0.5 * diff(ylimit) )
}#end if
xlimit = pretty.xylim(u=datum$toyear ,fracexp=0.0,is.log=FALSE)
ylimit.pft = pretty.xylim(u=thisvar[,,pftuse],fracexp=0.0,is.log=plog)
ylimit.all = pretty.xylim(u=thisvar[,,npft+1],fracexp=0.0,is.log=plog)
#---------------------------------------------------------------------------------#



#---------------------------------------------------------------------------------#
# Loop over plant functional types. #
#---------------------------------------------------------------------------------#
for (p in pftuse){
pftlab = paste0("pft-",sprintf("%2.2i",p))
for (p in pftplt){
if (p == (npft + 1)){
pftlab = "pft-00"
ylimit = ylimit.all
}else{
pftlab = paste0("pft-",sprintf("%2.2i",p))
ylimit = ylimit.pft
}#end if
cat0(" - ",pft$name[p],".")

if (plog){
xylog = "y"
ydrought = c( exp(sqrt(ylimit[1]^3/ylimit[2]))
, exp(sqrt(ylimit[2]^3/ylimit[1]))
)#end c
}else{
xylog = ""
ydrought = c( ylimit[1] - 0.5 * diff(ylimit)
, ylimit[2] + 0.5 * diff(ylimit) )
}#end if

#----- Loop over output formats. ----------------------------------------------#
for (o in sequence(nout)){
Expand Down
13 changes: 8 additions & 5 deletions ED/Template/scripts/odyssey/spawn_poly.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ moi=$(whoami)
#----- Description of this simulation, used to create unique job names. -------------------#
desc=$(basename ${here})
#----- Original and scratch main data paths. ----------------------------------------------#
#d_path="/n/home00/mlongo/data"
d_path="/n/moorcroftfs5/mlongo/data"
d_path="/n/home00/mlongo/data"
#d_path="/n/moorcroftfs5/mlongo/data"
#----- Path where biomass initialisation files are: ---------------------------------------#
bioinit="${d_path}/ed2_data/site_bio_data"
alsinit="${d_path}/ed2_data/lidar_spline_bio_data"
Expand All @@ -35,6 +35,8 @@ metmaindef="${d_path}/ed2_data"
packdatasrc="${d_path}/to_scratch"
#----- Path with land use scenarios. ------------------------------------------------------#
lumain="${d_path}/ed2_data/land_use"
#----- Path with other input data bases (soil texture, DGD, land mask, etc). --------------#
inpmain="${d_path}/ed2_data"
#----- Should the met driver be copied to local scratch disks? ----------------------------#
copy2scratch=false
#------------------------------------------------------------------------------------------#
Expand Down Expand Up @@ -63,10 +65,10 @@ optsrc="-n" # Option for .bashrc (for special submission setti
#----- Submit job automatically? (It may become false if something prevents submission). --#
submit=false
#----- Settings for this group of polygons. -----------------------------------------------#
global_queue="moorcroft_amd" # Queue
global_queue="huce_intel" # Queue
sim_memory=0 # Memory per simulation. Zero uses queue's default
n_cpt=8 # Number of cpus per task (it will be limited by maximum)
partial=true # Partial submission (false will ignore polya and npartial
n_cpt=12 # Number of cpus per task (it will be limited by maximum)
partial=false # Partial submission (false will ignore polya and npartial
# and send all polygons.
polya=21 # First polygon to submit
npartial=300 # Maximum number of polygons to include in this bundle
Expand Down Expand Up @@ -1836,6 +1838,7 @@ do
#---------------------------------------------------------------------------------------#
ED2IN="${here}/${polyname}/ED2IN"
sed -i~ s@paththere@${here}@g ${ED2IN}
sed -i~ s@myinpmain@${inpmain}@g ${ED2IN}
sed -i~ s@myyeara@${thisyeara}@g ${ED2IN}
sed -i~ s@mymontha@${montha}@g ${ED2IN}
sed -i~ s@mydatea@${datea}@g ${ED2IN}
Expand Down
3 changes: 3 additions & 0 deletions ED/Template/scripts/sdumont/spawn_poly.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,8 @@ shefhead='SHEF_NCEP_DRIVER_DS314'
metmain="${d_scratch}/ed2_data"
#----- Path with land use scenarios. ------------------------------------------------------#
lumain="${d_scratch}/lu_scenarios"
#----- Path with other input data bases (soil texture, DGD, land mask, etc). --------------#
inpmain="${d_scratch}/ed2_data"
#----- Memory per simulation. -------------------------------------------------------------#
sim_memory=8000
#------------------------------------------------------------------------------------------#
Expand Down Expand Up @@ -1701,6 +1703,7 @@ do
#---------------------------------------------------------------------------------------#
ED2IN="${here}/${polyname}/ED2IN"
sed -i~ s@paththere@${here}@g ${ED2IN}
sed -i~ s@myinpmain@${inpmain}@g ${ED2IN}
sed -i~ s@myyeara@${thisyeara}@g ${ED2IN}
sed -i~ s@mymontha@${montha}@g ${ED2IN}
sed -i~ s@mydatea@${datea}@g ${ED2IN}
Expand Down
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