CHANGELOG for Biome-BGCMuSo v6.1 2020-05-23 Dóra HIDY Changes from 6.0 to 6.0.1: - bug fixing in decomp.c (initalization of temporary variables) - bug fixing in daily_allocation.c (control of nitrogen pools to avoid negative pools) Changes from 6.0.1 to 6.0.2: - bug fixed in prephenology.c which caused a problem when original model phenology was used Changes from 6.0.2 to 6.0.3 - modification - change in the meaning of one parameter in the SOIL parameter block of the SOI file: instead of ratio of bare soil evaporation and pot. evaporation [DIM] alternative parameter in SOIL parameter block of SOI file: limit of first stage evaporation [mm] default value: 6 - modification: no .txt extension will be used if text output is selected (dayout extension will be used for all cases) - new output variables: 114 - ws->soil_evapCUM1 (Cumulative soil evaporation in first evaporation phase (no limit)) 115 - ws->soil_evapCUM2 (Cumulative soil evaporation in sencond evaporation phase (dsr limit)) 213 - wf->pot_infilt - bug fixing in plant height calculation (affecting only herbaceous simulations) - bug fixing in CH4-emission calculation (unit change, kg instead of g) - modification: no maintanance respiration will be present in case of the fruit pool of agroecosystems (i.e. crop yield is handled as inactive pool and cannot decrease with time due to maintenance respiration until harvest) - new routine: Joe Rithie's bare soil evaporation calculation is implemented (potEVAP_to_actEVAP.c) to simulate more relistic drying of the upper soil layers - modification: baresoil_evap.c - calculation of potential soil evaporation instead of actual evaporation - bug fixing in transient run - in previous versions endpoint file was not updated after the transient run Changes from 6.0.3 to 6.1 - improved hydrology calculations (improved soil evaporation calculation; sequence of processes are modified) - bug fixing related to simulations performed at the southen hemisphere (SH). 2th of July is considered as start for the calculations, which means that the first half of the first simulation year is skipped - introduction of new subroutines in the source code: date_to_DOY.c, pondANDrunoff.c - now it is possible to retrieve the model version with the comman muso.exe -v - bug fixing related to simulations performed at the southen hemisphere related to phenology (prephenology.c is affected) - calculation of yearday starts at 1 in the meteorology file - the transient run has its own output file: "_TRZ" is the output filename convention - option for modification of SWC content within the restart file: added control on initial soil water content in the normal run. the modification resolves inconsistency between spinup and normal simulation if soil parameters are changed - introduction of new output variables for the rooting zone (defined by maximum rooting depth): mean soil water content, available soil water content, drain water, mineralized N leaching, PSI - modified logic for the N and C content (result of laching) for the bottom (inactive) soil layer (400-1000 cm): the maximum amount of NH4+, NO3+, DOC and DON is fixed - new water scalar function in the nitrification calculation, based on water-filled pore space (WFPS; Parton et al. 2001, https://doi.org/10.1029/2001JD900101). extension of the SOIL file with new soil parameters for critical WFPS-values - WFPS is calculated based on saturated water content instead of bulk density and total porosity - modified photosynthesis stress simulation: introduction of non-stomatal effect on photosyntheis. according to the new feature soil water stress can down-regulate the carbon assimilation. note that up to version 6.1 C4 photosynthesis was NOT affected by stomatal aperture. this new feature enables an alternative control on photosynthesis in C3 and C4 plants as well. - introduction of a new EPC parameter: photoSTRESSeffect, that defines the effect of soil stress on photosynthesis (now this is line 110 in the EPC file; the rest of the lines are shifted accordingly) - introduction of new output variables: WFPS and pH scalar (see above) m_co2 (CO2 concentration multiplier) assim_Tcoeff (Tmax limitation factor of photosynthesis) assim_SScoeff (soil moisture stress limitation factor of photosynthesis) date of phenohphase changes (easy extraction of anthesis date) total aboveground woody biomass (storage/transfer pools are included, 3104) cumulative N leaching from the root zone (cum_NleachRZ, 3105) net greenhouse gas balance, NGB = NBP - N2Oflux(Ceq) - CH4flux(Ceq) N-limitation factors CH4_flux_TOTAL - total ecosystem CH4 flux SUM of potential N-immobilization (pot_immob, 1537) mhole plant mortality on the actual day (wpm_act, 2793) soilw (layer by layer) available for plants (119-128) cumulative soil respiration (3106) year-to-date maximum rooting depth [2674], Year-to-date maximum plant heigth [2675] plant type [24] (fallow:0, maize:1, wheat:2, barley:3, sunflower:4, canola:5, grass:6, unknown:-1) C:N ratio of litter and soil pools for all soil layers, all pool types [3107-3186] Living+dead abovegound biomass for non-woody and woody biomass with non-structured carbohydrate [3187-3188] Living abovegound biomass for non-woody and woody biomass with and without non-structured carbohydrate[3189-3192] Dead abovegound biomass for non-woody and woody biomass with and without non-structured carbohydrate[3193-3196] - modified soil stress calculation option: now it is based on transpiration deficit - bug fixing in photosynthesis.c: Tmax limitation of assimilation is corrected - bug fixing in transpiration calculation - bug fixing in CH4flux_estimation: WFPS maximization - introduction of a new parameter in the SOIL file (line 50): curvature of soil stress function. the new parameter is introduced to provide mechanism for soil texture dependent drought stress (caused by texture-specific matric potential) - modification: bottom boundary layer N-content is constant (set in SOI file) - new whole plant mortality (WPM) logic: as in the orgiginal Biome-BGC mortality is defined as average for the whole year (instead of growing season) - modified name for some output parameters : cum_runoff (3002), cum_WleachRZ (3003) - the unit of two management related parameters related to THINNING has changed: the proportion of the thinned woody and non-woody plant biomass is now in percent (%) instead of proportion (value between 0 and 1) - small adjustment of potential immobilization and minerazed N content in the rootzone: not all of the N-content of the deepest layer of the root zone is considered; rather, only a part is handled, weighted by the rooting depth in last layer - modified output parameter: total abovegound non-woody biomass C content (instead of non-woody+woody; abgC_nw; 3059) - modification of the daily allocation routine (daily_allocation.c): plant N-demand, soil N-availability and N-limitation are calculated layer by layer (instead of the whole rootzone that was implemented in previous versions) - modification of soil mineralized nitrogen calculation (multilayer_sminn.c): plant N-uptake is calculated layer by layer (instead of the whole rootzone that was implemented in previous versions) - modification of daily allocation routine during the spinup phase (daily_allocation.c): no artificial N addition to the mineralized N pool to meet plant demand in the spinup phase - extension of the log file with cumulative soil evaporation and transpiration value - introduction of a new soil parameter: aerodynamic resistance for bare soil evaporation calculation (this means a change in the soil file structure) - modification of the calculation of variables representing rooting zone (soil water content in rooting zone [117], available soil water content in rooting zone [118], volumetric soil water content in rooting zone [2634], soil matrix potential in rooting zone [2635], soil matrix potential in rooting zone [2635]: now the calculation is made for the actual root depth instead of the maximum rooting zone that was implemented in earlier model versions - modification of rooting depth calculation (multilayer_rootdeph.c): actual rooting depth is the function of the live fine root carbon content (instead of sum of live and dead fine root) - small bug fixing of root distribution calculation (multilayer_rootdeph.c) - small bug fixing in senesncence calculation - modification of conditional management initialization - small bug fixing in cut-down plant material to litter calculation (belowground cut-down dead biomass to litter) - small bug fixing in mortality calculation (belowground standing dead biomass to litter) - small bug fixing in output_map_init: variable 563 is Ndeepleach_snk (instead of Ndeepleach_snk) - modification in variable names: instead of CTDBc_transfer, CTDBn_transfer, STDBc_transfer, STDBn_transfer: CTDBc_nsc, CTDBn_nsc, STDBc_nsc, STDBn_nsc - small bug fixing in rootlenght proportion calculation (different for soil water calculation and litter decomposition) - small bug fixing in pond water calculation - correction of output variable names (depth of soil layers) - bug fixing in live wood turnover rates calculation (annual_rates.c) - modification of maximum spinup year parameter in INI file (TIME_DEFINE block): instead of maximum years of spinup run, maximum number of spinup cylces can be set. - new option in spinup control: if maximum number of spinup cylces is a positive number the spinup control is the function of soil carbon balance; if it is a negative number spinup control is determined by the maximum number of spinup cylces - differentiation of spinup tolerance parameter: woody - 0.0005, non-woody: 0.005.