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[3107-3126] 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. - small changes in error codes - small modification of GSI calculation condition in transient phase - small bug fixation in forest simulation (cutdown_to_litter.c) - modification of errorCode writing - new output variable: 2794 - flower_date - new output variable group - IMMOBratioAP layer 1 to layer 10 (2676 - 2685) - correction of output variable names - implementation of optional spinup N-addition: add N to sminn to meet demand layer by layer this function is optional: only if Ndep value has a negative sign in NDEP_CONTROL section of INI file - new function: mulch.c simply simulate the effect of mulch layer on soil: equalization of the temperature and the water content of the first (0-3 cm) and the second (3-10 cm) layers. - new output variables: aboveground biomass values - live, dead, with and without non-structured carbohydrate, woody, non-woody (3157-3168) - new output variables: rootzone values for soil and litter carbon/nitrogen content, mineralized nitrogen content (3169-3173) - correction of error messages (with error codes) - new routine: writeErrorCode.c - modification of litter decomposition (state_update.c and mortality.c - in previous MuSo versions litter contants only with the top soil layer (0-3 cm). From MuSo 6.1-b20 the first two layers participate in the decomposition of the litter and coarse woody debris (in order to decrease the nitrogen, water and temperature limitation during the decomposition). - modification of mortality.c and fire_mortality.c according to the original modell - introduction of dead stem combustion proportion parameter - modification of multilayer_leaching.c - in order to avoid N accumulation of bottom layer, the NH4/NO3/DOC/DON concentration of the bottom layer is maximized by the the concentration of the next layer (200-400 cm) instead of SOI parameter (critical value of dissolved N and C in bottom/inactive layer - bug correction in firstday.c: default value of germination layer is 0 (instead of 1). - small bug correction in co2 and ndep initalization files - modification of calculation: first day of phenological phases and flowering phenophase - small bug correction in C:N ratio calculation of litter and soil pools for all soil layers [3107-3126] - small bug correction in phenophase calculation (phenphase.c) - accumulated leafc carbon in the first phenphase - modification in cstate_init.c: if user defines max fruit/softstem C in INI file, but no fruit/softstem allocation in EPC file, max fruit/softstem C is set to 0. - bug correction of soil DOC leaching in multilayer_leaching.c - small correction in plouging calculation: nitrogen fluxes are calculated based on PLGceoff (instead of carbon fluxes and C:N ratio) - correction of C and N pool initialization of spinup phase (firstday.c) - correction of rootlength proportion initialization of evergreen biomes - correction of DaboveCnsc_nw and DaboveCnsc_w output variables (3167, 3168) - bug fixation in annual_rates.c - calculation of woody turnover_increment - specifying evergreen overrides any user input phenology data, and triggers a very simple treatment of the transfer, litterfall, and current growth signals. Treatment is the same for woody and non-woody types, and the same for model or user-input phenology */ - firstday.c:evergreen biome: root available also in the first day - correction of multilayer mineralized nitrogen, daily allocation and denitrification calculations - separate routine in multilayer_sminn.c: nitrification.c - correction of deep leaching of water, mineralized N, DOC and DON (bottom layer calculations) - modification of soil CN ratios in bgc_constant.h - possibility of normal run using CN_state block of INI file - possibility of using W_state block of INI file also in case of reading endpoint file - cumulative water and nitrogen stress variables - new variable: Nprec_snk - theoretical N sink from number representation error of nitrogen calculations - new summary output variables: CNlitr_total, CNsoil_total (3107, 3108) - new goup of summary output variables: maximum rooting zone variables (3169-3174): smin, soilC, soilN, litrC, litrN, sminNavail - SWX calculation in soiltress_calculation.c instead of senescence.c (also extreme temperature effect calculation remained in senescence.c) - m_SWCstressLENGTH variable instead of m_dsws (not equal to cum_SWCstress variable) - correction of genetically programmed leaf senescence - bug fixation - new feature: evaporation reduction in case of mulch coverage - onscreen information from the last simulation year (maxLAI, soilC, litrC) - modified estimation of hygroscopic water in sprop_init.c - new soil water function in decoposition calculation: trapezoidal function instead of triange (optimal above field capacity) - gross and net mineralization, potential and actual immobilization is calculated layer by layer and also summarized (2676-2703) - dead stem and coarse woody biomass combustion proportion in mortality.c (values from Biome-BGC v.1.1.) - cut-down and dead plant material divides into the 0-30 cm litter layers instead of getting into the top layer (cutdown2litter.c, mortality.c, senescence.c) - fire mortality affects litter pools in rooting zone (instead of only top layer) - fire_mortality.c - specifying evergreen overrides any user input phenology data, and triggers a simple treatment of the transfer, litterfall, and current growth signals (dayphen.c) - bug fixation in annual_rates.c - reading maximum allowable simulation cycles for spinup simulation instead of spinup years from RESTART_BLOCK of INI file - change in SOI file: line 19 - C:N ratio of stable (recalcitrant) SOM pool - small bug fixation in reading of INI file CN_state block - small bug fixation in fertilizing simulation (slurry) - small bug fixation in logfile (printout of available NO3 content of top soil layer) - new output variables: sum of litter and cwdc carbon and nitrogen content, and available mineralized N content in 0-30 cm [3072-3074] - small bug fixation in nsc_maintresp.c