diff --git a/RBBGCMuso/inst/examples/hhs/c3grass_muso6.epc b/RBBGCMuso/inst/examples/hhs/c3grass_muso6.epc new file mode 100644 index 0000000..2da9e60 --- /dev/null +++ b/RBBGCMuso/inst/examples/hhs/c3grass_muso6.epc @@ -0,0 +1,139 @@ +ECOPHYS FILE - C3 grass muso6 +---------------------------------------------------------------------------------------- +FLAGS +0 (flag) biome type flag (1 = WOODY 0 = NON-WOODY) +0 (flag) woody type flag (1 = EVERGREEN 0 = DECIDUOUS) +1 (flag) photosyn. type flag (1 = C3 PSN 0 = C4 PSN) +---------------------------------------------------------------------------------------- +PLANT FUNCTIONING PARAMETERS +0 (yday) yearday to start new growth (when phenology flag = 0) +364 (yday) yearday to end litterfall (when phenology flag = 0) +1.0 (prop.) transfer growth period as fraction of growing season (when transferGDD_flag = 0) +1.0 (prop.) litterfall as fraction of growing season (when transferGDD_flag = 0) +0 (Celsius) base temperature +-9999 (Celsius) minimum temperature for growth displayed on current day (-9999: no T-dependence) +-9999 (Celsius) optimal1 temperature for growth displayed on current day (-9999: no T-dependence) +-9999 (Celsius) optimal2 temperature for growth displayed on current day (-9999: no T-dependence) +-9999 (Celsius) maxmimum temperature for growth displayed on current day (-9999: no T-dependence) +-9999 (Celsius) minimum temperature for carbon assimilation on current day (-9999: no T-dependence) +-9999 (Celsius) optimal1 temperature for carbon assimilation on current day (-9999: no T-dependence) +-9999 (Celsius) optimal2 temperature for carbon assimilation on current day (-9999: no T-dependence) +-9999 (Celsius) maxmimum temperature for carbon assimilation on current day (-9999: no T-dependence) +1.0 (1/yr) annual leaf and fine root turnover fraction +0.00 (1/yr) annual live wood turnover fraction +0.0 (1/yr) annual fire mortality fraction +0.01 (1/vegper) whole-plant mortality fraction in vegetation period +36.6 (kgC/kgN) C:N of leaves +45.0 (kgC/kgN) C:N of leaf litter, after retranslocation +50.0 (kgC/kgN) C:N of fine roots +36.6 *(kgC/kgN) C:N of fruit +36.6 (kgC/kgN) C:N of soft stem +0.0 *(kgC/kgN) C:N of live wood +0.0 *(kgC/kgN) C:N of dead wood +0.4 (kgC/kgDM) dry matter carbon content of leaves +0.4 (kgC/kgDM) dry matter carbon content of leaf litter +0.4 (kgC/kgDM) dry matter carbon content of fine roots +0.4 *(kgC/kgDM) dry matter carbon content of fruit +0.4 (kgC/kgDM) dry matter carbon content of soft stem +0.4 *(kgC/kgDM) dry matter carbon content of live wood +0.4 *(kgC/kgDM) dry matter carbon content of dead wood +0.68 (DIM) leaf litter labile proportion +0.23 (DIM) leaf litter cellulose proportion +0.34 (DIM) fine root labile proportion +0.44 (DIM) fine root cellulose proportion +0.68 *(DIM) fruit litter labile proportion +0.23 *(DIM) fruit litter cellulose proportion +0.68 (DIM) soft stem litter labile proportion +0.23 (DIM) soft stem litter cellulose proportion +0.00 *(DIM) dead wood cellulose proportion +0.01 (1/LAI/d) canopy water interception coefficient +0.7 (DIM) canopy light extinction coefficient +0.6 (g/MJ) potential radiation use efficiency +0.781 (DIM) radiation parameter1 (Jiang et al.2015) +-13.596 (DIM) radiation parameter2 (Jiang et al.2015) +2.0 (DIM) all-sided to projected leaf area ratio +2.0 (DIM) ratio of shaded SLA:sunlit SLA +0.3 (DIM) fraction of leaf N in Rubisco +0.03 (DIM) fraction of leaf N in PEP Carboxylase +0.002 (m/s) maximum stomatal conductance (projected area basis) +0.00006 (m/s) cuticular conductance (projected area basis) +0.039 (m/s) boundary layer conductance (projected area basis) +1.0 (m) maximum height of plant +0.8 (kgC) stem weight corresponding to maximum height +0.5 (dimless) plant height function shape parameter (slope) +1.0 (m) maximum depth of rooting zone +2.67 (DIM) root distribution parameter +0.4 (kgC) root weight corresponding to max root depth +0.5 (dimless) root depth function shape parameter (slope) +1000 (m/kg) root weight to rooth length conversion factor +0.3 (prop.) growth resp per unit of C grown +0.195 (kgC/kgN/d) maintenance respiration in kgC/day per kg of tissue N +0.1 (DIM) theoretical maximum prop. of non-structural and structural carbohydrates +0.24 (DIM) prop. of non-structural carbohydrates available for maintanance respiration +0.0048 (kgN/m2/yr) symbiotic+asymbiotic fixation of N +0 (day) time delay for temperature in photosynthesis acclimation +---------------------------------------------------------------------------------------- +CROP SPECIFIC PARAMETERS +0 (DIM) number of phenophase of germination (from 1 to 7; 0: NO specific) +0 (DIM) number of phenophase of emergence (from 1 to 7; 0: NO specific) +0.5 (prop.) critical VWCratio (prop. to FC-WP) in germination +0 (DIM) number of phenophase of photoperiodic slowing effect (from 1 to 7; 0: NO effect) +20 (hour) critical photoslow daylength +0.005 (DIM) slope of relative photoslow development rate +0 (DIM) number of phenophase of vernalization (from 1 to 7; 0: NO effect) +0 (Celsius) critical vernalization temperature 1 +5 (Celsius) critical vernalization temperature 2 +8 (Celsius) critical vernalization temperature 3 +15 (Celsius) critical vernalization temperature 4 +0.04 (DIM) slope of relative vernalization development rate +50 (n) required vernalization days (in vernalization development rate) +0 (DIM) number of flowering phenophase (from 1 to 7;0: NO effect) +35 (Celsius) critical flowering heat stress temperature 1 +40 (Celsius) critical flowering heat stress temperature 2 +0.2 (prop.) theoretical maximum of flowering thermal stress mortality parameter +---------------------------------------------------------------------------------------- +STRESS AND SENESCENCE PARAMETERS +1.0 (prop) VWC ratio to calc. soil moisture limit 1 (prop. to FC-WP) +0.95 (prop) VWC ratio to calc. soil moisture limit 2 (prop. to SAT-FC) +0.4 (prop) minimum of soil moisture limit2 multiplicator (full anoxic stress value) +1000 (Pa) vapor pressure deficit: start of conductance reduction +2800 (Pa) vapor pressure deficit: complete conductance reduction +0.03 (prop.) maximum senescence mortality coefficient of aboveground plant material +0.02 (prop.) maximum senescence mortality coefficient of belowground plant material +0.01 (prop.) maximum senescence mortality coefficient of non-structured plant material +35 (Celsius) lower limit extreme high temperature effect on senescence mortality +40 (Celsius) upper limit extreme high temperature effect on senescence mortality +0.01 (prop.) turnover rate of wilted standing biomass to litter +0.047 (prop.) turnover rate of non-woody cut-down biomass to litter +0.01 (prop.) turnover rate of woody cut-down biomass to litter +30 (nday) drought tolerance parameter (critical value of DSWS) +0.2 (dimless) effect of soilstress factor on photosynthesis (1: full effect, 0: no effect) +---------------------------------------------------------------------------------------- +GROWING SEASON PARAMETERS +5 (kg/m2) crit. amount of snow limiting photosyn. +20 (Celsius) limit1 (under:full constrained) of HEATSUM index +60 (Celsius) limit2 (above:unconstrained) of HEATSUM index +0 (Celsius) limit1 (under:full constrained) of TMIN index +5 (Celsius) limit2 (above:unconstrained) of TMIN index +4000 (Pa) limit1 (above:full constrained) of VPD index +1000 (Pa) limit2 (under:unconstrained) of VPD index +0 (s) limit1 (under:full constrained) of DAYLENGTH index +0 (s) limit2 (above:unconstrained) of DAYLENGTH index +10 (day) moving average (to avoid the effects of extreme events) +0.10 (dimless) GSI limit1 (greater that limit -> start of vegper) +0.01 (dimless) GSI limit2 (less that limit -> end of vegper) +---------------------------------------------------------------------------------------- +PHENOLOGICAL (ALLOCATION) PARAMETERS (7 phenological phases) +phase1 phase2 phase3 phase4 phase5 phase6 phase7 (text) name of the phenophase +10000 200 500 200 400 200 100 (Celsius) length of phenophase (GDD) +0.3 0.3 0.3 0.3 0.3 0.3 0.3 (ratio) leaf ALLOCATION +0.5 0.5 0.5 0.5 0.5 0.5 0.5 (ratio) fine root ALLOCATION +0.0 0.0 0.0 0.0 0.0 0.0 0.0 (ratio) fruit ALLOCATION +0.2 0.2 0.2 0.2 0.2 0.2 0.2 (ratio) soft stem ALLOCATION +0 0 0 0 0 0 0 (ratio) live woody stem ALLOCATION +0 0 0 0 0 0 0 (ratio) dead woody stem ALLOCATION +0 0 0 0 0 0 0 (ratio) live coarse root ALLOCATION +0 0 0 0 0 0 0 (ratio) dead coarse root ALLOCATION +49 49 49 49 49 49 49 (m2/kgC) canopy average specific leaf area (projected area basis) +0.37 0.37 0.37 0.37 0.37 0.37 0.37 (prop.) current growth proportion +10000 10000 10000 10000 10000 10000 10000 (Celsius) maximal lifetime of plant tissue \ No newline at end of file diff --git a/RBBGCMuso/inst/examples/hhs/hhs.soi b/RBBGCMuso/inst/examples/hhs/hhs.soi new file mode 100644 index 0000000..16ca6f8 --- /dev/null +++ b/RBBGCMuso/inst/examples/hhs/hhs.soi @@ -0,0 +1,63 @@ +SOILPROP FILE - hhs muso6 +---------------------------------------------------------------------------------------- +NITROGEN AND DECOMPOSITION PARAMETERS +0.1 (prop.) denitrification rate per g of CO2 respiration of SOM +0.2 (prop.) nitrification coefficient 1 +0.07 (prop.) nitrification coefficient 2 +0.02 (prop.) coefficient of N2O emission of nitrification +0.1 (prop.) NH4 mobilen proportion +1.0 (prop.) NO3 mobilen proportion +10 (m) e-folding depth of decomposition rate's depth scalar +0.002 (prop.) fraction of dissolved part of SOIL1 organic matter +0.002 (prop.) fraction of dissolved part of SOIL2 organic matter +0.002 (prop.) fraction of dissolved part of SOIL3 organic matter +0.002 (prop.) fraction of dissolved part of SOIL4 organic matter +0.1 (prop.) minimum WFPS for scalar of nitrification calculation +0.45 (prop.) lower optimum WFPS for scalar of nitrification calculation +0.55 (prop.) higher optimum WFPS for scalar of nitrification calculation +0.2 (prop.) minimum value for saturated WFPS scalar of nitrification calculation +10 (ppm) critical value of dissolved N and C in bottom (inactive layer) +---------------------------------------------------------------------------------------- +RATE SCALARS +0.35 (prop) respiration fractions for fluxes between compartments (l1s1) +0.50 (prop) respiration fractions for fluxes between compartments (l2s2) +0.26 (prop) respiration fractions for fluxes between compartments (l4s3) +0.25 (prop) respiration fractions for fluxes between compartments (s1s2) +0.41 (prop) respiration fractions for fluxes between compartments (s2s3) +0.50 (prop) respiration fractions for fluxes between compartments (s3s4) +0.7 (1/day) rate constant scalar of labile litter pool +0.07 (1/day) rate constant scalar of cellulose litter pool +0.014 (1/day) rate constant scalar of lignin litter pool +0.07 (1/day) rate constant scalar of fast microbial recycling pool +0.014 (1/day) rate constant scalar of medium microbial recycling pool +0.0014 (1/day) rate constant scalar of slow microbial recycling pool +0.0001 (1/day) rate constant scalar of recalcitrant SOM (humus) pool +0.001 (1/day) rate constant scalar of physical fragmentation of coarse woody debris +---------------------------------------------------------------------------------------- +CH4 PARAMETERS +212.5 (DIM) soil CH4 emission bulk density dependence parameter1 +1.81 (DIM) soil CH4 emission bulk density dependence parameter2 +-1.353 (DIM) soil CH4 emission soil water content dependence parameter1 +0.2 (DIM) soil CH4 emission soil water content dependence parameter2 +1.781 (DIM) soil CH4 emission soil water content dependence parameter3 +6.786 (DIM) soil CH4 emission soil water content dependence parameter4 +0.010 (DIM) soil CH4 emission soil temperature dependence parameter1 +---------------------------------------------------------------------------------------- +SOIL PARAMETERS +2 (m) depth of soil +6 (mm) limit of first stage evaporation +20.00 (mm) maximum height of pond water +1 (dimless) curvature of soil stress function +-9999 (dimless) measured runoff curve number (-9999: no measured data, model estimation) +---------------------------------------------------------------------------------------- +SOIL COMPOSITION AND CHARACTERISTIC VALUES (-9999: no measured data) +30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 (%) sand percentage by volume in rock-free soil +50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 (%) silt percentage by volume in rock-free soil +7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 (dimless) soil pH (dimless) measured runoff curve number +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (g/cm3) bulk density +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at saturation +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at field capacity +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at wilting point +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at hygroscopic water content +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (dimless) drainage coefficient +-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (cm/day) hydraulic condictivity at saturation \ No newline at end of file diff --git a/RBBGCMuso/inst/examples/hhs/muso.exe b/RBBGCMuso/inst/examples/hhs/muso.exe new file mode 100644 index 0000000..972e841 Binary files /dev/null and b/RBBGCMuso/inst/examples/hhs/muso.exe differ diff --git a/RBBGCMuso/inst/examples/hhs/parameters.csv b/RBBGCMuso/inst/examples/hhs/parameters.csv new file mode 100644 index 0000000..fd2dee0 --- /dev/null +++ b/RBBGCMuso/inst/examples/hhs/parameters.csv @@ -0,0 +1,15 @@ +ABREVIATION,INDEX,min,max MuSo6 +TRANSFERGROWTHP,11,0.1,1 +T_BASE,13,0,8 +WPM,25,0,0.1 +CN_leaf,26,14.3,58.8 +CWIC,49,0.01,0.07 +CLEC,50,0.3,0.8 +FLNR,56,0.1,0.2 +MSTOMACOND,58,0.001,0.007 +ROOTDEPTH,64,0.5,3 +ROOTDISTRIB,65,0.2,5 +RELSWCCRIT1,96,0.97,1 +RELSWCCRIT2,97,0.4,1 +SENESCENCABG,101,0,0.1 +SLA,137.60,10,60