Couple BMST to vegetation phenology of Bgc #1
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added 5 commits
September 3, 2018 15:35
…Bgc module if active: -Added variables leaf and stem mass index -Parameter reading moved to pftconMod.F90 because some are also needed in CNVegStructUpdateMod.F90 -Stem heat storage suppressed if breast-height diameter below 0.01 m -Fraction of radiation recieved by stem is now calculated according to stem surface area instead of exposed stem area index
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Oct 24, 2018
added summary N litterfall flux variable
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Apr 10, 2020
Use svg rather than the default png for math images
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Sep 14, 2020
Minor fixes for bioenergy branch
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Sep 14, 2020
update my ctsm fork to latest
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Sep 29, 2020
Changes to review of dynlakes_master_notools Response to review of Pull Request ESCOMP#1109: including removal of lake_heat variable, update of surfrd_lakemask module and clean up of comments.
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Apr 15, 2022
Ideally we would do year-2000 tests to have more crop cover and thus potentially be more useful tests. However, there are problems running a year-2000 ciso test with crop. These problems exist even with an SMS test on master: I tried tests like SMS_Ly1_P72x1.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput, but both debug & non-debug, intel & gnu versions. Debug tests fail like this (from SMS_D_Ly1_P72x1.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput): 30:Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation. 30: 30:Backtrace for this error: 13: 13:Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation. 13: 13:Backtrace for this error: 13:#0 0x2b9d1acc4aff in ??? 30:#0 0x2b9d1acc4aff in ??? 13:#1 0xf63fff in cisofluxcalc 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:1555 30:#1 0xf63fff in cisofluxcalc 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:1555 30:#2 0xf6b489 in __cncisofluxmod_MOD_cisoflux1 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:153 13:#2 0xf6b489 in __cncisofluxmod_MOD_cisoflux1 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNCIsoFluxMod.F90:153 13:#3 0xe45657 in __cndrivermod_MOD_cndrivernoleaching 13: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNDriverMod.F90:559 30:#3 0xe45657 in __cndrivermod_MOD_cndrivernoleaching 30: at /glade/work/sacks/ctsm_code/ctsm/src/biogeochem/CNDriverMod.F90:559 An intel test dies in the same place. Non-debug versions die like this (both for gnu and intel): 30: set_curr_delta ERROR: found unexpected non-zero delta mid-year 30: Dribbler name: hrv_xsmrpool_to_atm_c_13 30: i, delta = 2 NaN 30: Start of time step date (yr, mon, day, tod) = 2000 1 15 57600 30: This indicates that some non-zero flux was generated at a time step 30: other than the first time step of the year, which this dribbler was told not to expect. 30: If this non-zero mid-year delta is expected, then you can suppress this error 30: by setting allows_non_annual_delta to .true. when constructing this dribbler. 30:iam = 30: local gridcell index = 2 30:iam = 30: global gridcell index = 103 30:iam = 30: gridcell longitude = 285.0000000 30:iam = 30: gridcell latitude = -10.0000000 30: ENDRUN: 30: ERROR: set_curr_delta: found unexpected non-zero delta mid-year: ERROR in /glade/work/sacks/ctsm_code/ctsm/src/utils/AnnualFluxDr ibbler.F90 at line 276 So there is some issue with year-2000 ciso tests with crop. This issue exists on master, for clm45 and clm50 tests. (e.g., for clm50, I tried SMS_D_Ly1_P72x1.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput.)
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CanopyFluxesMod.F90 now uses the vegetation phenology of the Bgc-module when active. This required the following modifications:
Adding two new vegetation state variables: Stem mass index and leaf mass index (SMI and LMI). These variables are defined in CanopyStateType.F90. They are calculated in the CNVegStructUpdateMod.F90 in Bgc mode or in CanopyFluxesMod.F90 in Sp mode.
The parameter reading was moved to pftconMod.F90 because some of the parameters are also needed in CNVegStructUpdateMod.F90. This also resulted in slight modifications of readParamsMod.F90, clninitializeMod.F90, clm_instMod.F90, and namelist_definition_clm4_5.xml.
Stem heat storage is suppressed if breast-height diameter is below 0.01 m to avoid instabilities for small trees.
Additional (minor modifications):
CNVegStructUpdateMod.F90 now uses the tree number density of the parameter file instead of the hard coded constant tree number density
The fraction of radiation received by stem is now calculated according to stem surface area instead of exposed stem area index in CanopyFluxesMod.F90
When calculating the update in the stem temperature an additional if statement was added to avoid dividing by zero.