diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index f86a330408..e769d3187c 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -25,6 +25,7 @@ a9d96219902cf609636886c7073a84407f450d9a d866510188d26d51bcd6d37239283db690af7e82 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7 e096358c832ab292ddfd22dd5878826c7c788968 +475831f0fb0e31e97f630eac4e078c886558b61c # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index ec10de5080..84caf92465 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -1,18 +1,18 @@ ============================= CTSM History Fields (fates) ============================= - + CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: use_cn = F use_crop = F use_fates = T - -=================================== ================ ============================================================================================== ================================================================= ======= + +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Variable Name Level Dim. Long Description Units Active? -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T AGLB - Aboveground leaf biomass kg/m^2 F @@ -22,13 +22,27 @@ ALTMAX - maximum annual active layer ALTMAX_LASTYEAR - maximum prior year active layer thickness m F ATM_O3 - atmospheric ozone partial pressure mol/mol F ATM_TOPO - atmospheric surface height m T +AZSUN - azimuth angle of the sun radians F AnnET - Annual ET mm/s F BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BCPHIDRY - black carbon deposition (phidry) from atmosphere kg/m^2/s F +BCPHIWET - black carbon deposition (phiwet) from atmosphere kg/m^2/s F +BCPHODRY - black carbon deposition (phodry) from atmosphere kg/m^2/s F BTRAN - transpiration beta factor unitless T BTRANMN - daily minimum of transpiration beta factor unitless T +CH4PROD - Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT - aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT - aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT - diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT - diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT - ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT - ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T COL_CTRUNC - column-level sink for C truncation gC/m^2 F COL_NTRUNC - column-level sink for N truncation gN/m^2 F -COSZEN - cosine of solar zenith angle none F +COSZEN - cosine of solar zenith angle (downscaled if downscaling is activated) none F +COSZEN_GRC - cosine of solar zenith angle none F CROPPROD1C - 1-yr crop product (grain+biofuel) C gC/m^2 T CROPPROD1C_LOSS - loss from 1-yr crop product pool gC/m^2/s T CROPPROD1N - 1-yr crop product (grain+biofuel) N gN/m^2 T @@ -43,7 +57,15 @@ DPVLTRB3 - turbulent deposition veloci DPVLTRB4 - turbulent deposition velocity 4 m/s F DSL - dry surface layer thickness mm T DSTDEP - total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTDRY1 - dust deposition (dry1) from atmosphere kg/m^2/s F +DSTDRY2 - dust deposition (dry2) from atmosphere kg/m^2/s F +DSTDRY3 - dust deposition (dry3) from atmosphere kg/m^2/s F +DSTDRY4 - dust deposition (dry4) from atmosphere kg/m^2/s F DSTFLXT - total surface dust emission kg/m2/s T +DSTWET1 - dust deposition (wet1) from atmosphere kg/m^2/s F +DSTWET2 - dust deposition (wet2) from atmosphere kg/m^2/s F +DSTWET3 - dust deposition (wet3) from atmosphere kg/m^2/s F +DSTWET4 - dust deposition (wet4) from atmosphere kg/m^2/s F DWT_CROPPROD1C_GAIN - landcover change-driven addition to 1-year crop product pool gC/m^2/s T DWT_CROPPROD1N_GAIN - landcover change-driven addition to 1-year crop product pool gN/m^2/s T DWT_PROD100C_GAIN - landcover change-driven addition to 100-yr wood product pool gC/m^2/s F @@ -52,6 +74,7 @@ DWT_PROD10C_GAIN - landcover change-driven add DWT_PROD10N_GAIN - landcover change-driven addition to 10-yr wood product pool gN/m^2/s F DWT_WOODPRODC_GAIN - landcover change-driven addition to wood product pools gC/m^2/s T DWT_WOODPRODN_GAIN - landcover change-driven addition to wood product pools gN/m^2/s T +DYN_COL_ADJUSTMENTS_CH4 - Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F DYN_COL_SOIL_ADJUSTMENTS_NH4 - Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F @@ -95,10 +118,6 @@ FATES_DAYSINCE_COLDLEAFON - site-level days elapsed sin FATES_DEMOTION_CARBONFLUX - demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1 T FATES_DISTURBANCE_RATE_FIRE - disturbance rate from fire m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_LOGGING - disturbance rate from logging m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_P2P - disturbance rate from primary to primary lands m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_P2S - disturbance rate from primary to secondary lands m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_POTENTIAL - potential (i.e., including unresolved) disturbance rate m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_S2S - disturbance rate from secondary to secondary lands m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_TREEFALL - disturbance rate from treefall m2 m-2 yr-1 T FATES_EFFECT_WSPEED - effective wind speed for fire spread in meters per second m s-1 T FATES_EXCESS_RESP - respiration of un-allocatable carbon gain kg m-2 s-1 T @@ -128,6 +147,7 @@ FATES_HARVEST_DEBT - Accumulated carbon failed t FATES_HARVEST_DEBT_SEC - Accumulated carbon failed to be harvested from secondary patches kg C T FATES_HET_RESP - heterotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_IGNITIONS - number of successful fire ignitions per m2 land area per second m-2 s-1 T +FATES_L2FR - The leaf to fineroot biomass multiplier for target allometry kg kg-1 T FATES_LAI - leaf area index per m2 land area m2 m-2 T FATES_LAI_SECONDARY - leaf area index per m2 land area, secondary patches m2 m-2 T FATES_LBLAYER_COND - mean leaf boundary layer conductance mol m-2 s-1 T @@ -139,7 +159,7 @@ FATES_LITTER_OUT - litter flux out in kg carbo FATES_LSTEMMAINTAR - live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_MAINT_RESP - maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T FATES_MAINT_RESP_SECONDARY - maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T -FATES_MAINT_RESP_UNREDUCED - diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F +FATES_MAINT_RESP_UNREDUCED - diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 T FATES_MORTALITY_CFLUX_CANOPY - flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T FATES_MORTALITY_CFLUX_USTORY - flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T FATES_NCHILLDAYS - site-level number of chill days days T @@ -148,6 +168,7 @@ FATES_NCOHORTS_SECONDARY - total number of cohorts per FATES_NCOLDDAYS - site-level number of cold days days T FATES_NEP - net ecosystem production in kg carbon per m2 per second kg m-2 s-1 T FATES_NESTEROV_INDEX - nesterov fire danger index T +FATES_NIR_RAD_ERROR - mean two-stream solver error for NIR - T FATES_NONSTRUCTC - non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2 kg m-2 T FATES_NPATCHES - total number of patches per site T FATES_NPATCHES_SECONDARY - total number of patches per site T @@ -155,7 +176,6 @@ FATES_NPP - net primary production in k FATES_NPP_SECONDARY - net primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T FATES_PRIMARY_PATCHFUSION_ERR - error in total primary lands associated with patch fusion m2 m-2 yr-1 T FATES_PROMOTION_CARBONFLUX - promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1 T -FATES_RAD_ERROR - radiation error in FATES RTM W m-2 T FATES_REPROC - total biomass in live plant reproductive tissues in kg carbon per m2 kg m-2 T FATES_ROS - fire rate of spread in meters per second m s-1 T FATES_SAPWOODC - total biomass in live plant sapwood in kg carbon per m2 kg m-2 T @@ -181,8 +201,12 @@ FATES_UNGERM_SEED_BANK - ungerminated seed mass of a FATES_USTORY_VEGC - biomass of understory plants in kg carbon per m2 land area kg m-2 T FATES_VEGC - total biomass in live plants in kg carbon per m2 land area kg m-2 T FATES_VEGC_ABOVEGROUND - aboveground biomass in kg carbon per m2 land area kg m-2 T +FATES_VIS_RAD_ERROR - mean two-stream solver error for VIS - T FATES_WOOD_PRODUCT - total wood product from logging in kg carbon per m2 land area kg m-2 T FCEV - canopy evaporation W/m^2 T +FCH4 - Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 - Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT - CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T FCO2 - CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F FCOV - fractional impermeable area unitless T FCTR - canopy transpiration W/m^2 T @@ -194,6 +218,8 @@ FGR_R - Rural heat flux into soil/s FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F FH2OSFC - fraction of ground covered by surface water unitless T FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED - fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG - time-lagged inundated fraction of vegetated columns unitless F FIRA - net infrared (longwave) radiation W/m^2 T FIRA_ICE - net infrared (longwave) radiation (ice landunits only) W/m^2 F FIRA_R - Rural net infrared (longwave) radiation W/m^2 T @@ -202,8 +228,9 @@ FIRE - emitted infrared (longwave) FIRE_ICE - emitted infrared (longwave) radiation (ice landunits only) W/m^2 F FIRE_R - Rural emitted infrared (longwave) radiation W/m^2 T FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F -FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T -FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FLDS - atmospheric longwave radiation (downscaled for glacier and hillslope columns) W/m^2 T +FLDS_ICE - atmospheric longwave radiation (downscaled for glacier and hillslope columns) (ice landunits o W/m^2 F +FLDS_NOT_DOWNSCALED - atmospheric longwave radiation (pre-downscaling) W/m^2 F FPG - fraction of potential gpp proportion T FPI - fraction of potential immobilization proportion T FROST_TABLE - frost table depth (natural vegetated and crop landunits only) m F @@ -214,7 +241,7 @@ FSA_R - Rural absorbed solar radiat FSA_U - Urban absorbed solar radiation W/m^2 F FSD24 - direct radiation (last 24hrs) K F FSD240 - direct radiation (last 240hrs) K F -FSDS - atmospheric incident solar radiation W/m^2 T +FSDS - atmospheric incident solar radiation (downscaled for glacier and hillslope columns) W/m^2 T FSDSND - direct nir incident solar radiation W/m^2 T FSDSNDLN - direct nir incident solar radiation at local noon W/m^2 T FSDSNI - diffuse nir incident solar radiation W/m^2 T @@ -222,6 +249,7 @@ FSDSVD - direct vis incident solar r FSDSVDLN - direct vis incident solar radiation at local noon W/m^2 T FSDSVI - diffuse vis incident solar radiation W/m^2 T FSDSVILN - diffuse vis incident solar radiation at local noon W/m^2 T +FSDS_from_atm - atmospheric incident solar radiation received from atmosphere (pre-downscaling) W/m^2 T FSH - sensible heat not including correction for land use change and rain/snow conversion W/m^2 T FSH_G - sensible heat from ground W/m^2 T FSH_ICE - sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F @@ -320,7 +348,7 @@ LIT_MET_N - LIT_MET N LIT_MET_N_1m - LIT_MET N to 1 meter gN/m^2 F LIT_MET_N_TO_SOM_ACT_N - decomp. of metabolic litter N to active soil organic N gN/m^2 F LNC - leaf N concentration gN leaf/m^2 T -LWdown - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWdown - atmospheric longwave radiation (downscaled for glacier and hillslope columns) W/m^2 F LWup - upwelling longwave radiation W/m^2 F MORTALITY_CROWNAREA_CANOPY - Crown area of canopy trees that died m2/ha/year T MORTALITY_CROWNAREA_UNDERSTORY - Crown aera of understory trees that died m2/ha/year T @@ -337,13 +365,19 @@ M_SOM_PAS_N_TO_LEACHING - passive soil organic N leac M_SOM_SLO_C_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F M_SOM_SLO_N_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T +NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T NET_NMIN - net rate of N mineralization gN/m^2/s T NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T NSUBSTEPS - number of adaptive timesteps in CLM timestep unitless F OBU - Monin-Obukhov length m F OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T +OCPHIDRY - organic carbon deposition (phidry) from atmosphere kg/m^2/s F +OCPHIWET - organic carbon deposition (phiwet) from atmosphere kg/m^2/s F +OCPHODRY - black carbon deposition (phodry) from atmosphere kg/m^2/s F PARVEGLN - absorbed par by vegetation at local noon W/m^2 T -PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PBOT - atmospheric pressure at surface (downscaled for glacier and hillslope columns) Pa T +PBOT_NOT_DOWNSCALED - atmospheric pressure at surface (pre-downscaling) Pa F +PCH4 - atmospheric partial pressure of CH4 Pa T PCO2 - atmospheric partial pressure of CO2 Pa T POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T POT_F_DENIT - potential denitrification flux gN/m^2/s T @@ -356,10 +390,11 @@ PROD10C - 10-yr wood product C PROD10C_LOSS - loss from 10-yr wood product pool gC/m^2/s F PROD10N - 10-yr wood product N gN/m^2 F PROD10N_LOSS - loss from 10-yr wood product pool gN/m^2/s F -PSurf - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +PSurf - atmospheric pressure at surface (downscaled for glacier and hillslope columns) Pa F Q2M - 2m specific humidity kg/kg T QAF - canopy air humidity kg/kg F QBOT - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QBOT_NOT_DOWNSCALED - atmospheric specific humidity (pre-downscaling) kg/kg F QDIRECT_THROUGHFALL - direct throughfall of liquid (rain + above-canopy irrigation) mm/s F QDIRECT_THROUGHFALL_SNOW - direct throughfall of snow mm/s F QDRAI - sub-surface drainage mm/s T @@ -396,6 +431,7 @@ QIRRIG_FROM_GW_UNCONFINED - water added through unconfi QIRRIG_FROM_SURFACE - water added through surface water irrigation mm/s T QIRRIG_SPRINKLER - water added via sprinkler irrigation mm/s F QOVER - total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG - time-lagged surface runoff for soil columns mm/s F QPHSNEG - net negative hydraulic redistribution flux mm/s F QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T QRUNOFF - total liquid runoff not including correction for land use change mm/s T @@ -436,7 +472,7 @@ RAW2 - aerodynamical resistance RB - leaf boundary resistance s/m F RH - atmospheric relative humidity % F RH2M - 2m relative humidity % T -RH2M_R - Rural 2m specific humidity % F +RH2M_R - Rural 2m relative humidity % F RH2M_U - Urban 2m relative humidity % F RHAF - fractional humidity of canopy air fraction F RH_LEAF - fractional humidity at leaf surface fraction F @@ -444,6 +480,7 @@ RSCANOPY - canopy resistance RSSHA - shaded leaf stomatal resistance s/m T RSSUN - sunlit leaf stomatal resistance s/m T Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rho_from_atm - atmospheric density (pre-downscaling) kg/m^3 F Rnet - net radiation W/m^2 F SABG - solar rad absorbed by ground W/m^2 T SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T @@ -546,21 +583,24 @@ T10 - 10-day running mean of 2-m TAF - canopy air temperature K F TAUX - zonal surface stress kg/m/s^2 T TAUY - meridional surface stress kg/m/s^2 T -TBOT - atmospheric air temperature (downscaled to columns in glacier regions) K T +TBOT - atmospheric air temperature (downscaled for glacier and hillslope columns) K T TBUILD - internal urban building air temperature K T TBUILD_MAX - prescribed maximum interior building temperature K F +TDEPTH - tributary water depth m F +TDEPTHMAX - tributary bankfull water depth m F TFLOOR - floor temperature K F TG - ground temperature K T TG_ICE - ground temperature (ice landunits only) K F TG_R - Rural ground temperature K F TG_U - Urban ground temperature K F TH2OSFC - surface water temperature K T -THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T +THBOT - atmospheric air potential temperature (downscaled for glacier and hillslope columns) K T TKE1 - top lake level eddy thermal conductivity W/(mK) T TLAI - total projected leaf area index m^2/m^2 T TOPO_COL - column-level topographic height m F TOPO_COL_ICE - column-level topographic height (ice landunits only) m F TOTCOLC - total column carbon, incl veg and cpool but excl product pools gC/m^2 T +TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T TOTCOLN - total column-level N, excluding product pools gN/m^2 T TOTECOSYSC - total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T TOTECOSYSN - total ecosystem N, excluding product pools gN/m^2 T @@ -600,8 +640,9 @@ TV - vegetation temperature TV24 - vegetation temperature (last 24hrs) K F TV240 - vegetation temperature (last 240hrs) K F TWS - total water storage mm T -Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair - atmospheric air temperature (downscaled for glacier and hillslope columns) K F Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F +Thair_from_atm - atmospheric air potential temperature (pre-downscaling) K F U10 - 10-m wind m/s T U10_DUST - 10-m wind for dust model m/s T U10_ICE - 10-m wind (ice landunits only) m/s F @@ -611,6 +652,7 @@ URBAN_AC - urban air conditioning flux URBAN_HEAT - urban heating flux W/m^2 T USTAR - aerodynamical resistance s/m F UST_LAKE - friction velocity (lakes only) m/s F +UWIND - atmospheric U wind velocity magnitude m/s F VA - atmospheric wind speed plus convective velocity m/s F VENTILATION - sensible heat flux from building ventilation W/m^2 T VOLR - river channel total water storage m3 T @@ -618,11 +660,13 @@ VOLRMCH - river channel main channel VPD - vpd Pa F VPD2M - 2m vapor pressure deficit Pa T VPD_CAN - canopy vapor pressure deficit kPa T +VWIND - atmospheric V wind velocity magnitude m/s F WASTEHEAT - sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T WBT - 2 m Stull Wet Bulb C T WBT_R - Rural 2 m Stull Wet Bulb C T WBT_U - Urban 2 m Stull Wet Bulb C T WIND - atmospheric wind velocity magnitude m/s T +WTGQ - surface tracer conductance m/s T Wind - atmospheric wind velocity magnitude m/s F Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F Z0MG - roughness length over ground, momentum (vegetated landunits only) m F @@ -633,6 +677,7 @@ ZBOT - atmospheric reference heigh ZETA - dimensionless stability parameter unitless F ZII - convective boundary height m F ZWT - water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T num_iter - number of iterations unitless F QICE_FORC elevclas qice forcing sent to GLC mm/s F @@ -660,39 +705,28 @@ FATES_SCORCH_HEIGHT_APPF fates_levagepft SPITFIRE flame Scorch Heigh FATES_VEGC_APPF fates_levagepft biomass per PFT in each age bin in kg carbon per m2 kg m-2 F FATES_MORTALITY_AGESCEN_AC fates_levcacls age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T FATES_NPLANT_AC fates_levcacls number of plants per m2 by cohort age class m-2 T -FATES_CROWNAREA_CL fates_levcan total crown area in each canopy layer m2 m-2 T -FATES_FABD_SHA_TOPLF_CL fates_levcan shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABD_SUN_TOPLF_CL fates_levcan sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SHA_TOPLF_CL fates_levcan shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SUN_TOPLF_CL fates_levcan sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F -FATES_LAISHA_TOP_CL fates_levcan LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F -FATES_LAISUN_TOP_CL fates_levcan LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F -FATES_PARSHA_Z_CL fates_levcan PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F -FATES_PARSUN_Z_CL fates_levcan PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F +FATES_CROWNAREA_CL fates_levcan area fraction of the canopy footprint occupied by each canopy-leaf layer m2 m-2 T +FATES_LAISHA_CL fates_levcan LAI of shaded leaves by canopy layer m2 m-2 F +FATES_LAISUN_CL fates_levcan LAI of sunlit leaves by canopy layer m2 m-2 F +FATES_PARSHA_CL fates_levcan PAR absorbed by shaded leaves in each canopy layer W m-2 F +FATES_PARSUN_CL fates_levcan PAR absorbed by sunlit leaves in each canopy layer W m-2 F FATES_MORTALITY_AGESCEN_ACPF fates_levcapf age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F FATES_NPLANT_ACPF fates_levcapf stem number density by pft and age class m-2 F -FATES_CROWNAREA_CLLL fates_levcnlf total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F -FATES_FABD_SHA_CLLL fates_levcnlf shade fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABD_SUN_CLLL fates_levcnlf sun fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SHA_CLLL fates_levcnlf shade fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SUN_CLLL fates_levcnlf sun fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_LAISHA_Z_CLLL fates_levcnlf LAI in the shade by each canopy and leaf layer m2 m-2 F -FATES_LAISUN_Z_CLLL fates_levcnlf LAI in the sun by each canopy and leaf layer m2 m-2 F +FATES_CROWNAREA_CLLL fates_levcnlf area fraction of the total ground occupied by each canopy-leaf layer m2 m-2 F +FATES_LAISHA_CLLL fates_levcnlf LAI in the shade by each canopy and leaf layer m2 m-2 F +FATES_LAISUN_CLLL fates_levcnlf LAI in the sun by each canopy and leaf layer m2 m-2 F FATES_NET_C_UPTAKE_CLLL fates_levcnlf net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F FATES_PARPROF_DIF_CLLL fates_levcnlf radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F FATES_PARPROF_DIR_CLLL fates_levcnlf radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F -FATES_PARSHA_Z_CLLL fates_levcnlf PAR absorbed in the shade by each canopy and leaf layer W m-2 F -FATES_PARSUN_Z_CLLL fates_levcnlf PAR absorbed in the sun by each canopy and leaf layer W m-2 F -FATES_FABD_SHA_CLLLPF fates_levcnlfpf shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABD_SUN_CLLLPF fates_levcnlfpf sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SHA_CLLLPF fates_levcnlfpf shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SUN_CLLLPF fates_levcnlfpf sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_LAISHA_Z_CLLLPF fates_levcnlfpf LAI in the shade by each canopy, leaf, and PFT m2 m-2 F -FATES_LAISUN_Z_CLLLPF fates_levcnlfpf LAI in the sun by each canopy, leaf, and PFT m2 m-2 F +FATES_PARSHA_CLLL fates_levcnlf PAR absorbed in the shade by each canopy and leaf layer W m-2 F +FATES_PARSUN_CLLL fates_levcnlf PAR absorbed in the sun by each canopy and leaf layer W m-2 F +FATES_CROWNFRAC_CLLLPF fates_levcnlfpf area fraction of the canopy footprint occupied by each canopy-leaf-pft layer m2 m-2 F +FATES_LAISHA_CLLLPF fates_levcnlfpf Shaded leaf area by each canopy, leaf, and PFT m2 m-2 F +FATES_LAISUN_CLLLPF fates_levcnlfpf Sunlit leaf area by each canopy, leaf, and PFT m2 m-2 F FATES_PARPROF_DIF_CLLLPF fates_levcnlfpf radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F FATES_PARPROF_DIR_CLLLPF fates_levcnlfpf radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F -FATES_PARSHA_Z_CLLLPF fates_levcnlfpf PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F -FATES_PARSUN_Z_CLLLPF fates_levcnlfpf PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F +FATES_PARSHA_CLLLPF fates_levcnlfpf PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F +FATES_PARSUN_CLLLPF fates_levcnlfpf PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F FATES_CWD_ABOVEGROUND_DC fates_levcwdsc debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F FATES_CWD_ABOVEGROUND_IN_DC fates_levcwdsc debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F FATES_CWD_ABOVEGROUND_OUT_DC fates_levcwdsc debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F @@ -718,6 +752,8 @@ FATES_FUEL_BURNT_BURNFRAC_FC fates_levfuel product of fraction (0-1) o FATES_FUEL_MOISTURE_FC fates_levfuel spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T FATES_CANOPYAREA_HT fates_levheight canopy area height distribution m2 m-2 T FATES_LEAFAREA_HT fates_levheight leaf area height distribution m2 m-2 T +FATES_PATCHAREA_LU fates_levlanduse patch area by land use type m2 m-2 T +FATES_DISTURBANCE_RATE_MATRIX_LULU fates_levlulu disturbance rates by land use type x land use type matrix m2 m-2 yr-1 T FATES_CANOPYCROWNAREA_PF fates_levpft total PFT-level canopy-layer crown area per m2 land area m2 m-2 T FATES_CROWNAREA_PF fates_levpft total PFT-level crown area per m2 land area m2 m-2 T FATES_DAYSINCE_DROUGHTLEAFOFF_PF fates_levpft PFT-level days elapsed since drought leaf drop days T @@ -726,14 +762,17 @@ FATES_DROUGHT_STATUS_PF fates_levpft PFT-level drought status, < FATES_ELONG_FACTOR_PF fates_levpft PFT-level mean elongation factor (partial flushing/abscission) 1 T FATES_GPP_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T FATES_GPP_SE_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_L2FR_CANOPY_REC_PF fates_levpft The leaf to fineroot biomass multiplier for recruits (canopy) kg kg-1 T +FATES_L2FR_USTORY_REC_PF fates_levpft The leaf to fineroot biomass multiplier for recruits (understory) kg kg-1 T FATES_LEAFC_PF fates_levpft total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T FATES_MEANLIQVOL_DROUGHTPHEN_PF fates_levpft PFT-level mean liquid water volume for drought phenolgy m3 m-3 T FATES_MEANSMP_DROUGHTPHEN_PF fates_levpft PFT-level mean soil matric potential for drought phenology Pa T FATES_MORTALITY_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T -FATES_MORTALITY_CSTARV_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T +FATES_MORTALITY_CSTARV_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality (both kg m-2 s-1 T FATES_MORTALITY_FIRE_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T FATES_MORTALITY_HYDRO_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T FATES_MORTALITY_PF fates_levpft PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_MORT_CSTARV_CONT_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality (Cont kg m-2 s-1 T FATES_NPLANT_PF fates_levpft total PFT-level number of individuals per m2 land area m-2 T FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of individuals per m2 land area, secondary patches m-2 T FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 s-1 T @@ -776,8 +815,8 @@ FATES_LEAF_ALLOC_CANOPY_SZ fates_levscls allocation to leaves for ca FATES_LEAF_ALLOC_USTORY_SZ fates_levscls allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F FATES_LSTEMMAINTAR_CANOPY_SZ fates_levscls live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F FATES_LSTEMMAINTAR_USTORY_SZ fates_levscls live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F -FATES_M3_MORTALITY_CANOPY_SZ fates_levscls C starvation mortality of canopy plants by size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZ fates_levscls C starvation mortality of understory plants by size N/ha/yr F +FATES_M3_MORTALITY_CANOPY_SZ fates_levscls C starvation mortality of canopy plants by size m-2 yr-1 F +FATES_M3_MORTALITY_USTORY_SZ fates_levscls C starvation mortality of understory plants by size m-2 yr-1 F FATES_MAINTAR_CANOPY_SZ fates_levscls maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F FATES_MAINTAR_USTORY_SZ fates_levscls maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F FATES_MORTALITY_AGESCEN_SE_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T @@ -787,7 +826,7 @@ FATES_MORTALITY_BACKGROUND_SZ fates_levscls background mortality by siz FATES_MORTALITY_CANOPY_SE_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T FATES_MORTALITY_CANOPY_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T FATES_MORTALITY_CSTARV_SE_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_CSTARV_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year (both continous and te m-2 yr-1 T FATES_MORTALITY_FIRE_SZ fates_levscls fire mortality by size in number of plants per m2 per year m-2 yr-1 T FATES_MORTALITY_FREEZING_SE_SZ fates_levscls freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T FATES_MORTALITY_FREEZING_SZ fates_levscls freezing mortality by size in number of plants per m2 per year m-2 yr-1 T @@ -798,7 +837,7 @@ FATES_MORTALITY_LOGGING_SE_SZ fates_levscls logging mortality by size i FATES_MORTALITY_LOGGING_SZ fates_levscls logging mortality by size in number of plants per m2 per year m-2 yr-1 T FATES_MORTALITY_SENESCENCE_SE_SZ fates_levscls senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T FATES_MORTALITY_SENESCENCE_SZ fates_levscls senescence mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_TERMINATION_SZ fates_levscls termination mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_TERMINATION_SZ fates_levscls termination mortality (excluding C-starvation) by size in number of plants per m2 per year m-2 yr-1 T FATES_MORTALITY_USTORY_SZ fates_levscls total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T FATES_NPLANT_CANOPY_SZ fates_levscls number of canopy plants per m2 by size class m-2 T FATES_NPLANT_SZ fates_levscls number of plants per m2 by size class m-2 T @@ -845,6 +884,8 @@ FATES_BGSAPMAINTAR_SZPF fates_levscpf below-ground sapwood mainte FATES_BGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_BGSTRUCT_ALLOC_SZPF fates_levscpf allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_C13DISC_SZPF fates_levscpf C13 discrimination by pft/size per mil F +FATES_CROWNAREA_CANOPY_SZPF fates_levscpf Total crown area of canopy plants by pft/size m2 m-2 F +FATES_CROWNAREA_USTORY_SZPF fates_levscpf Total crown area of understory plants by pft/size m2 m-2 F FATES_DDBH_CANOPY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F FATES_DDBH_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F FATES_DDBH_USTORY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F @@ -863,22 +904,22 @@ FATES_LEAFC_CANOPY_SZPF fates_levscpf biomass in leaves of canopy FATES_LEAFC_SZPF fates_levscpf leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F FATES_LEAFC_USTORY_SZPF fates_levscpf biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F FATES_LEAF_ALLOC_SZPF fates_levscpf allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_M3_MORTALITY_CANOPY_SZPF fates_levscpf C starvation mortality of canopy plants by pft/size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZPF fates_levscpf C starvation mortality of understory plants by pft/size N/ha/yr F +FATES_M3_MORTALITY_CANOPY_SZPF fates_levscpf C starvation mortality of canopy plants by pft/size m-2 yr-1 F +FATES_M3_MORTALITY_USTORY_SZPF fates_levscpf C starvation mortality of understory plants by pft/size m-2 yr-1 F FATES_MAINTAR_SZPF fates_levscpf maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F FATES_MORTALITY_AGESCEN_SZPF fates_levscpf age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_BACKGROUND_SZPF fates_levscpf background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_CAMBIALBURN_SZPF fates_levscpf fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_CANOPY_SZPF fates_levscpf total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_CROWNSCORCH_SZPF fates_levscpf fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CSTARV_SZPF fates_levscpf carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CSTARV_SZPF fates_levscpf carbon starvation mortality by pft/size in number of plants per m2 per year (both continous an m-2 yr-1 F FATES_MORTALITY_FIRE_SZPF fates_levscpf fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_FREEZING_SZPF fates_levscpf freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_HYDRAULIC_SZPF fates_levscpf hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_IMPACT_SZPF fates_levscpf impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_LOGGING_SZPF fates_levscpf logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_SENESCENCE_SZPF fates_levscpf senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_TERMINATION_SZPF fates_levscpf termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_TERMINATION_SZPF fates_levscpf termination mortality (excluding C-starvation) by pft/size in number pf plants per m2 per year m-2 yr-1 F FATES_MORTALITY_USTORY_SZPF fates_levscpf total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_NPLANT_CANOPY_SZPF fates_levscpf number of canopy plants by size/pft per m2 m-2 F FATES_NPLANT_SZPF fates_levscpf stem number density by pft/size m-2 F @@ -1008,8 +1049,11 @@ ratio_k1 levdcmp ratio_k1 ratio_no3_co2 levdcmp ratio_no3_co2 ratio F soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F +CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T SOILPSI levgrnd soil water potential in each soil layer MPa F TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T @@ -1035,6 +1079,8 @@ SNO_TK_ICE levsno Thermal conductivity (ice l SNO_T_ICE levsno Snow temperatures (ice landunits only) K F SNO_Z levsno Snow layer thicknesses m F SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F +CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T FATES_FRAGMENTATION_SCALER_SL levsoi factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T FATES_FROOTC_SL levsoi Total carbon in live plant fine-roots over depth kg m-3 T H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 89e7dd23fc..67868f75b1 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -8,11 +8,11 @@ use_cn = T use_crop = T use_fates = F -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Variable Name Level Dim. Long Description Units Active? -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= A10TMIN - 10-day running mean of min 2-m temperature K F A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T @@ -36,10 +36,14 @@ ATM_O3 - atmospheric ozone partial p ATM_TOPO - atmospheric surface height m T AVAILC - C flux available for allocation gC/m^2/s F AVAIL_RETRANSN - N flux available from retranslocation pool gN/m^2/s F +AZSUN - azimuth angle of the sun radians F AnnET - Annual ET mm/s F BAF_CROP - fractional area burned for crop s-1 T BAF_PEATF - fractional area burned in peatland s-1 T BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BCPHIDRY - black carbon deposition (phidry) from atmosphere kg/m^2/s F +BCPHIWET - black carbon deposition (phiwet) from atmosphere kg/m^2/s F +BCPHODRY - black carbon deposition (phodry) from atmosphere kg/m^2/s F BETA - coefficient of convective velocity none F BGLFR - background litterfall rate 1/s F BGNPP - belowground NPP gC/m^2/s T @@ -66,7 +70,8 @@ COL_NTRUNC - column-level sink for N tru COST_NACTIVE - Cost of active uptake gN/gC T COST_NFIX - Cost of fixation gN/gC T COST_NRETRANS - Cost of retranslocation gN/gC T -COSZEN - cosine of solar zenith angle none F +COSZEN - cosine of solar zenith angle (downscaled if downscaling is activated) none F +COSZEN_GRC - cosine of solar zenith angle none F CPHASE - crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T CPOOL - temporary photosynthate C pool gC/m^2 T CPOOL_DEADCROOT_GR - dead coarse root growth respiration gC/m^2/s F @@ -158,7 +163,15 @@ DPVLTRB3 - turbulent deposition veloci DPVLTRB4 - turbulent deposition velocity 4 m/s F DSL - dry surface layer thickness mm T DSTDEP - total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTDRY1 - dust deposition (dry1) from atmosphere kg/m^2/s F +DSTDRY2 - dust deposition (dry2) from atmosphere kg/m^2/s F +DSTDRY3 - dust deposition (dry3) from atmosphere kg/m^2/s F +DSTDRY4 - dust deposition (dry4) from atmosphere kg/m^2/s F DSTFLXT - total surface dust emission kg/m2/s T +DSTWET1 - dust deposition (wet1) from atmosphere kg/m^2/s F +DSTWET2 - dust deposition (wet2) from atmosphere kg/m^2/s F +DSTWET3 - dust deposition (wet3) from atmosphere kg/m^2/s F +DSTWET4 - dust deposition (wet4) from atmosphere kg/m^2/s F DT_VEG - change in t_veg, last iteration K F DWT_CONV_CFLUX - conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T DWT_CONV_CFLUX_DRIBBLED - conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T @@ -246,8 +259,9 @@ FIRE - emitted infrared (longwave) FIRE_ICE - emitted infrared (longwave) radiation (ice landunits only) W/m^2 F FIRE_R - Rural emitted infrared (longwave) radiation W/m^2 T FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F -FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T -FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FLDS - atmospheric longwave radiation (downscaled for glacier and hillslope columns) W/m^2 T +FLDS_ICE - atmospheric longwave radiation (downscaled for glacier and hillslope columns) (ice landunits o W/m^2 F +FLDS_NOT_DOWNSCALED - atmospheric longwave radiation (pre-downscaling) W/m^2 F FPI - fraction of potential immobilization proportion T FPSN - photosynthesis umol m-2 s-1 T FPSN24 - 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F @@ -278,7 +292,7 @@ FSA_R - Rural absorbed solar radiat FSA_U - Urban absorbed solar radiation W/m^2 F FSD24 - direct radiation (last 24hrs) K F FSD240 - direct radiation (last 240hrs) K F -FSDS - atmospheric incident solar radiation W/m^2 T +FSDS - atmospheric incident solar radiation (downscaled for glacier and hillslope columns) W/m^2 T FSDSND - direct nir incident solar radiation W/m^2 T FSDSNDLN - direct nir incident solar radiation at local noon W/m^2 T FSDSNI - diffuse nir incident solar radiation W/m^2 T @@ -286,6 +300,7 @@ FSDSVD - direct vis incident solar r FSDSVDLN - direct vis incident solar radiation at local noon W/m^2 T FSDSVI - diffuse vis incident solar radiation W/m^2 T FSDSVILN - diffuse vis incident solar radiation at local noon W/m^2 T +FSDS_from_atm - atmospheric incident solar radiation received from atmosphere (pre-downscaling) W/m^2 T FSH - sensible heat not including correction for land use change and rain/snow conversion W/m^2 T FSH_G - sensible heat from ground W/m^2 T FSH_ICE - sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F @@ -426,6 +441,7 @@ LEAFC_STORAGE_XFER_ACC - Accumulated leaf C transfer LEAFC_TO_BIOFUELC - leaf C to biofuel C gC/m^2/s T LEAFC_TO_LITTER - leaf C litterfall gC/m^2/s F LEAFC_TO_LITTER_FUN - leaf C litterfall used by FUN gC/m^2/s T +LEAFC_TO_REMOVEDRESIDUEC - leaf C to removed residue C gC/m^2/s F LEAFC_XFER - leaf C transfer gC/m^2 F LEAFC_XFER_TO_LEAFC - leaf C growth from storage gC/m^2/s F LEAFN - leaf N gN/m^2 T @@ -487,6 +503,7 @@ LIVESTEMC_STORAGE - live stem C storage LIVESTEMC_STORAGE_TO_XFER - live stem C shift storage to transfer gC/m^2/s F LIVESTEMC_TO_BIOFUELC - livestem C to biofuel C gC/m^2/s T LIVESTEMC_TO_DEADSTEMC - live stem C turnover gC/m^2/s F +LIVESTEMC_TO_REMOVEDRESIDUEC - livestem C to removed residue C gC/m^2/s F LIVESTEMC_XFER - live stem C transfer gC/m^2 F LIVESTEMC_XFER_TO_LIVESTEMC - live stem C growth from storage gC/m^2/s F LIVESTEMN - live stem N gN/m^2 T @@ -498,7 +515,7 @@ LIVESTEMN_XFER - live stem N transfer LIVESTEMN_XFER_TO_LIVESTEMN - live stem N growth from storage gN/m^2/s F LIVESTEM_MR - live stem maintenance respiration gC/m^2/s F LNC - leaf N concentration gN leaf/m^2 T -LWdown - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWdown - atmospheric longwave radiation (downscaled for glacier and hillslope columns) W/m^2 F LWup - upwelling longwave radiation W/m^2 F MEG_acetaldehyde - MEGAN flux kg/m2/sec T MEG_acetic_acid - MEGAN flux kg/m2/sec T @@ -700,6 +717,9 @@ NUPTAKE_NPP_FRACTION - frac of NPP used in N uptak N_ALLOMETRY - N allocation index none F OBU - Monin-Obukhov length m F OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T +OCPHIDRY - organic carbon deposition (phidry) from atmosphere kg/m^2/s F +OCPHIWET - organic carbon deposition (phiwet) from atmosphere kg/m^2/s F +OCPHODRY - black carbon deposition (phodry) from atmosphere kg/m^2/s F OFFSET_COUNTER - offset days counter days F OFFSET_FDD - offset freezing degree days counter C degree-days F OFFSET_FLAG - offset flag none F @@ -719,8 +739,9 @@ PAR24_sun - sunlit PAR (24 hrs) PARVEGLN - absorbed par by vegetation at local noon W/m^2 T PAR_shade - shade PAR umol/m2/s F PAR_sun - sunlit PAR umol/m2/s F -PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PBOT - atmospheric pressure at surface (downscaled for glacier and hillslope columns) Pa T PBOT_240 - 10 day running mean of air pressure Pa F +PBOT_NOT_DOWNSCALED - atmospheric pressure at surface (pre-downscaling) Pa F PCH4 - atmospheric partial pressure of CH4 Pa T PCO2 - atmospheric partial pressure of CO2 Pa T PCO2_240 - 10 day running mean of CO2 pressure Pa F @@ -754,10 +775,11 @@ PSNSHA - shaded leaf photosynthesis PSNSHADE_TO_CPOOL - C fixation from shaded canopy gC/m^2/s T PSNSUN - sunlit leaf photosynthesis umolCO2/m^2/s T PSNSUN_TO_CPOOL - C fixation from sunlit canopy gC/m^2/s T -PSurf - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +PSurf - atmospheric pressure at surface (downscaled for glacier and hillslope columns) Pa F Q2M - 2m specific humidity kg/kg T QAF - canopy air humidity kg/kg F QBOT - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QBOT_NOT_DOWNSCALED - atmospheric specific humidity (pre-downscaling) kg/kg F QDIRECT_THROUGHFALL - direct throughfall of liquid (rain + above-canopy irrigation) mm/s F QDIRECT_THROUGHFALL_SNOW - direct throughfall of snow mm/s F QDRAI - sub-surface drainage mm/s T @@ -839,7 +861,7 @@ RETRANSN - plant pool of retranslocate RETRANSN_TO_NPOOL - deployment of retranslocated N gN/m^2/s T RH - atmospheric relative humidity % F RH2M - 2m relative humidity % T -RH2M_R - Rural 2m specific humidity % F +RH2M_R - Rural 2m relative humidity % F RH2M_U - Urban 2m relative humidity % F RH30 - 30-day running mean of relative humidity % F RHAF - fractional humidity of canopy air fraction F @@ -849,6 +871,7 @@ RR - root respiration (fine root RSSHA - shaded leaf stomatal resistance s/m T RSSUN - sunlit leaf stomatal resistance s/m T Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rho_from_atm - atmospheric density (pre-downscaling) kg/m^3 F Rnet - net radiation W/m^2 F SABG - solar rad absorbed by ground W/m^2 T SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T @@ -977,9 +1000,11 @@ T10 - 10-day running mean of 2-m TAF - canopy air temperature K F TAUX - zonal surface stress kg/m/s^2 T TAUY - meridional surface stress kg/m/s^2 T -TBOT - atmospheric air temperature (downscaled to columns in glacier regions) K T +TBOT - atmospheric air temperature (downscaled for glacier and hillslope columns) K T TBUILD - internal urban building air temperature K T TBUILD_MAX - prescribed maximum interior building temperature K F +TDEPTH - tributary water depth m F +TDEPTHMAX - tributary bankfull water depth m F TEMPAVG_T2M - temporary average 2m air temperature K F TEMPMAX_RETRANSN - temporary annual max of retranslocated N pool gN/m^2 F TEMPSUM_POTENTIAL_GPP - temporary annual sum of potential GPP gC/m^2/yr F @@ -992,7 +1017,7 @@ TG_ICE - ground temperature (ice lan TG_R - Rural ground temperature K F TG_U - Urban ground temperature K F TH2OSFC - surface water temperature K T -THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T +THBOT - atmospheric air potential temperature (downscaled for glacier and hillslope columns) K T THIC - 2 m Temp Hum Index Comfort C T THIC_R - Rural 2 m Temp Hum Index Comfort C T THIC_U - Urban 2 m Temp Hum Index Comfort C T @@ -1060,8 +1085,9 @@ TV240 - vegetation temperature (las TVEGD10 - 10 day running mean of patch daytime vegetation temperature Kelvin F TVEGN10 - 10 day running mean of patch night-time vegetation temperature Kelvin F TWS - total water storage mm T -Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair - atmospheric air temperature (downscaled for glacier and hillslope columns) K F Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F +Thair_from_atm - atmospheric air potential temperature (pre-downscaling) K F U10 - 10-m wind m/s T U10_DUST - 10-m wind for dust model m/s T U10_ICE - 10-m wind (ice landunits only) m/s F @@ -1072,6 +1098,7 @@ URBAN_AC - urban air conditioning flux URBAN_HEAT - urban heating flux W/m^2 T USTAR - aerodynamical resistance s/m F UST_LAKE - friction velocity (lakes only) m/s F +UWIND - atmospheric U wind velocity magnitude m/s F VA - atmospheric wind speed plus convective velocity m/s F VCMX25T - canopy profile of vcmax25 umol/m2/s T VENTILATION - sensible heat flux from building ventilation W/m^2 T @@ -1081,6 +1108,7 @@ VOLRMCH - river channel main channel VPD - vpd Pa F VPD2M - 2m vapor pressure deficit Pa T VPD_CAN - canopy vapor pressure deficit kPa T +VWIND - atmospheric V wind velocity magnitude m/s F Vcmx25Z - canopy profile of vcmax25 predicted by LUNA model umol/m2/s T WASTEHEAT - sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T WBA - 2 m Wet Bulb C T @@ -1261,7 +1289,7 @@ STEM_PROF levdcmp profile for litter C and N SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F WFPS levdcmp WFPS percent F anaerobic_frac levdcmp anaerobic_frac m3/m3 F -diffus levdcmp diffusivity (from nitrification-denitrification) m^2/s F +diffus levdcmp diffusivity m^2/s F fr_WFPS levdcmp fr_WFPS fraction F n2_n2o_ratio_denit levdcmp n2_n2o_ratio_denit gN/gN F r_psi levdcmp r_psi m F diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 86dabe609d..2c2aebad52 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -14,7 +14,7 @@ # -- import local classes for this script from ctsm.site_and_regional.base_case import BaseCase, USRDAT_DIR, DatmFiles -from ctsm.utils import add_tag_to_filename +from ctsm.utils import add_tag_to_filename, ensure_iterable logger = logging.getLogger(__name__) @@ -415,7 +415,10 @@ def modify_surfdata_atpoint(self, f_orig): # f_mod["PCT_CROP"][:, :] = 0 # -- loop over all dom_pft and pct_pft - zip_pfts = zip(self.dom_pft, self.pct_pft, self.cth, self.cbh) + iterable_length = len(self.dom_pft) + cth_to_zip = ensure_iterable(self.cth, iterable_length) + cbh_to_zip = ensure_iterable(self.cbh, iterable_length) + zip_pfts = zip(self.dom_pft, self.pct_pft, cth_to_zip, cbh_to_zip) for dom_pft, pct_pft, cth, cbh in zip_pfts: if cth is not None: f_mod["MONTHLY_HEIGHT_TOP"][:, :, :, dom_pft] = cth diff --git a/python/ctsm/test/test_unit_singlept_data_surfdata.py b/python/ctsm/test/test_unit_singlept_data_surfdata.py index a29fa05b33..2106799a4b 100755 --- a/python/ctsm/test/test_unit_singlept_data_surfdata.py +++ b/python/ctsm/test/test_unit_singlept_data_surfdata.py @@ -47,8 +47,8 @@ class TestSinglePointCaseSurfaceNoCrop(unittest.TestCase): evenly_split_cropland = False pct_pft = None num_pft = 16 - cth = [0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9] - cbh = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1] + cth = 0.9 + cbh = 0.1 include_nonveg = False uni_snow = True cap_saturation = True @@ -668,8 +668,8 @@ class TestSinglePointCaseSurfaceCrop(unittest.TestCase): evenly_split_cropland = False pct_pft = None num_pft = 78 - cth = [0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9, 0.9] - cbh = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1] + cth = 0.9 + cbh = 0.1 include_nonveg = False uni_snow = False cap_saturation = False diff --git a/python/ctsm/test/test_unit_utils.py b/python/ctsm/test/test_unit_utils.py index 85ba2515dd..aed43cfede 100755 --- a/python/ctsm/test/test_unit_utils.py +++ b/python/ctsm/test/test_unit_utils.py @@ -9,7 +9,7 @@ import os from ctsm import unit_testing -from ctsm.utils import fill_template_file +from ctsm.utils import fill_template_file, ensure_iterable from ctsm.config_utils import lon_range_0_to_360, _handle_config_value # Allow names that pylint doesn't like, because otherwise I find it hard @@ -328,6 +328,38 @@ def test_handleConfigValue_isListFalse(self): self.assertEqual(val_out, float(val_in)) +class TestUtilsEnsureIterable(unittest.TestCase): + """Tests of utils: ensure_iterable""" + + def test_ensure_iterable_number(self): + """ + Tests that ensure_iterable(NUMBER, 3) produces a list of 3 NUMBERs + """ + val = 724.1987 + self.assertEqual(ensure_iterable(val, 3), [val, val, val]) + + def test_ensure_iterable_none(self): + """ + Tests that ensure_iterable(None, 2) produces a list of 2 Nones + """ + val = None + self.assertEqual(ensure_iterable(val, 2), [val, val]) + + def test_ensure_iterable_already(self): + """ + Tests that ensure_iterable() returns the input if it's already iterable + """ + val = [11, 12] + self.assertEqual(ensure_iterable(val, 2), val) + + def test_ensure_iterable_error_wrong_length(self): + """ + Tests that ensure_iterable() errors if input is iterable but of the wrong length + """ + with self.assertRaisesRegex(ValueError, "Input is iterable but wrong length"): + ensure_iterable([11, 12], 3) + + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 8578ea860c..a5a02a5c9d 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -26,6 +26,24 @@ def abort(errmsg): sys.exit("ERROR: {}".format(errmsg)) +def ensure_iterable(thing_we_want_iterable, iterable_length): + """ + Ensure that a variable is iterable + """ + already_iterable = True + try: + iter(thing_we_want_iterable) + except TypeError: + already_iterable = False + + if not already_iterable: + thing_we_want_iterable = [thing_we_want_iterable] * iterable_length + elif len(thing_we_want_iterable) != iterable_length: + raise ValueError("Input is iterable but wrong length") + + return thing_we_want_iterable + + def fill_template_file(path_to_template, path_to_final, substitutions): """Given a template file (based on python's template strings), write a copy of the file with template values filled in. diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index ddb57d88f7..e90caeecbb 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -226,7 +226,7 @@ subroutine InitHistory(this, bounds) this%azsun_grc(begg:endg) = spval call hist_addfld1d (fname='AZSUN', units='radians', & - avgflag='A', long_name='cosine of solar zenith angle', & + avgflag='A', long_name='azimuth angle of the sun', & ptr_lnd=this%azsun_grc, default='inactive') this%coszen_grc(begg:endg) = spval diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index dd556a2df6..f91aaca761 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -346,7 +346,7 @@ subroutine InitBulkHistory(this, bounds) fname=this%info%fname('RH2M_R'), & units='%', & avgflag='A', & - long_name=this%info%lname('Rural 2m specific humidity'), & + long_name=this%info%lname('Rural 2m relative humidity'), & ptr_patch=this%rh_ref2m_r_patch, set_spec=spval, default='inactive') this%rh_ref2m_u_patch(begp:endp) = spval