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Pasim User Guide.pasim_v5.3_dec_2012

1. kg C m kg C m kg C m kg C m kg C m kg N m kg N m kg N m kg N m kg N m kg N m m m Soil will be highly better simulated with 6 soil layers Does not change Does not change Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Should not be higher than saturated value 6 0 1 076 0 66 0 001 0 814 0 052 0 001 0 001 0 001 0 001 0 001 0 001 0 00025 0 00035 Table 11 the soil tab parameters in expert mode 55 3 10 The expert mode The graphical interface can be used in an expert mode This mode allows the user to modify more parameters in the soil tab cf Figure 17 and in the properties tab cf Figure 18 Estimate parameters 1 2 Name Number of soil layers Parameter For the determination of the field capacity Parameter a for Freundlich equation for soil NH4 partitioning Parameter b for Freundlich equation for soil NH4 partitioning Initial cond For C in structural dead plant material kg C m Initial cond for C in metabolic dead plant material kg C m2 Initial cond for C in active soil organic matter kg Cim Initial cond For C in slow soil organic matter kg C m2 Initial cond for C in passive soil organic matter kg C m Initial cond for N in
2. Fractional C content of root structural dry matter kg C kg Soil depth below which there is neither plant N uptake nor soil texture effect of active SOM decomposition m Development stage at which ear emergence starts Activate autocalculation of root profile Parameter b used in calculation of root profile Fraction of structural dry root matter in soil layer h one value per soil layer Light saturated leaf photosynthetic rate at 20 C for vegetative stage umol m 2 s 1 Light saturated leaf photosynthetic rate at 20 C for reproductive stage umol m 2 s 1 Parameter a for soil NH4 partitioning Parameter b for soil NH4 partitioning Parameter to specify loss fraction at cutting events Fraction of digestible fibers in total fibers in age class 1 to 4 of lamina Fraction of digestible fibers in total fibers in age class 1 to 4 of stem Fraction of digestible fibers in total fibers in age class 1 to 4 of ear Number of PaSim files for spatialized simulations Number of grid points for spatialized simulations Number of possible grid points for spatialized simulations 2NB_POINTS TERRE Number of the grid point that will be run Use when initial conditions for SOM are unknown Else put NONE Used in equilibrium search Put NONE when running the model from SOM equilibrium or measurements values Do not change Do not change Useless if FLAG _ROOT PROFILE 0 0 05 Permanent Sown
3. 11 2 tr 2 Exemple 55 52 60 20 3600 2 11 360 0 24 Tr or 0 2 11 Tr or 0 2 11 Soil will be highly better simulated with 6 soil layers First layer must be 20 mm Must be larger than previous soil layer Does not change Sum of all layers has to be 1 All the same or increasing values could be estimated thanks to the following formula 1 dendity 2 65 Same as last layer Use soil routine Same as last layer Use soil routine Same as last layer Use soil routine NOT USED ANYMORE NOT USED ANYMORE Use soil routine Use soil routine Does not change Does not change Table 3 Description of site specific variables needed in PaSim input ADVISED VALUE 12 12 0 0 0 0 2 0 2 0 6 0 4 0 0 2 0 01 7 0 1 076 0 66 15 2 1 1 3 Site specific file This file Tab 3 and Figure 3 describes the site characteristics as well as the vegetation and soil properties However vegetation and soil properties for initialization and management will be defined in the initial condition file Also some of these parameters can be modified into the run file An example of a site specific file is given below To parameterize the soil a soil routine Figure 2 has been developed by Pierluigi Calanca Research Scientist at Agroscope Reckenholz Tanikon Research Station ART Zurich Switzerland This routine needs the number the depth the texture and the water saturation of ea
4. Forage quantity 0000000000 The specific file for the input data file e g names _files_input_site1_year1_cut txt must have the following form paths Input conditions site1 site_spe par Input conditions site1 init_cond par Input conditions site1_year1 management_cut dat Input meteo Ta dat Input meteo ea dat Input meteo u dat Input meteo IATMtot dat Input meteo Pa dat Input meteo NH3 dat Input meteo CO2 dat 30 31 2 In the PaSim run file you have activate e FLAG_FERTILIZATION 1 e FLAG_AUTOGESTION 1 e RESTART FILE IN restart txt e RESTART_ FILE OUT restart_site1_year1_cut txt and to specify the path of the names files_ input_sitel_year1_cut txt file At the end of the simulation which does not last more than a single year simulation PaSim creates a new file which contains the optimal forage DM yield This file is in the same directory than those of the automatic cutting management file The name of this file is derived from those of the automatic cutting management file by adding _yield_inn at its end e g site1_year1 management_cut_yield_inn dat NB Values of the forage DM yield must divided by 10 to be converted into t DM ha For running the second step automatic grazing on yearl 1 you have to create e 1PaSim specific run file e g sitel_yeari_graz pasim e 1 specific management file e g site1_year1 management_ graz dat e 1 specific file for input data file
5. wst 4_C14 llam 1 llam 2 llam 3 llam 4 Ist 1 Ist 2 Ist 3 Ist 4 tsoil 1 tsoil 2 tsoil 3 tsoil 4 tsoil 5 tsoil 6 ssw snow thetas 1 thetas 2 thetas 3 thetas 4 thetas 5 thetas 6 C14 or C13 fraction in lamina shoot structural dry matter in first age component lamina shoot structural dry matter in second age component C14 or C13 fraction in lamina shoot structural dry matter in second age component lamina shoot structural dry matter in third age component C14 or C13 fraction in lamina shoot structural dry matter in third age component lamina shoot structural dry matter in fourth age component C14 or C13 fraction in lamina shoot structural dry matter in fourth age component ear shoot structural dry matter in first age component C14 or C13 fraction in ear shoot structural dry matter in first age component ear shoot structural dry matter in second age component C14 or C13 fraction in ear shoot structural dry matter in second age component ear shoot structural dry matter in third age component C14 or C13 fraction in ear shoot structural dry matter in third age component ear shoot structural dry matter in fourth age component C14 or C13 fraction in ear shoot structural dry matter in fourth age component stem shoot structural dry matter in first age component C14 or C13 fraction in stem shoot structural dry matter in first age component stem shoot structural dry matter in second age component C14 or C13 fraction in stem
6. l interface de la seconde couche 7 dn20_3 d riv e de nn2o l interface de la troisi me couche 7 dn20_4 d riv e de nn2o a l interface de la quatrieme couche 7 dn20_5 d riv e de nn2o l interface de la 5 me couche 7 dn20_6 d riv e de nn2o l interface de la 6 me couche 7 dn2onitrif_1 dn2onitrif l interface de la premiere couche 7 dn2onitrif_2 dn2onitrif l interface de la seconde couche 7 dn2onitrif_3 dn2onitrif l interface de la troisi me couche 7 dn2onitrif_4 dn2onitrif l interface de la quatri me couche 7 dn2onitrif 5 dn2onitrif l interface de la 5 me couche 7 dn2onitrif 6 dn2onitrif l interface de la 6 me couche 7 DNDF total fraction of digestible fibres in shoot 7 DNDF fraction of digestible fibres in total fibres 7 DNDFI amount of digestible fibres in the animal s intake Digestible Neutral Detergent Fiber Intake kg d 1 7 dNstruct daily Nitrogen variation in structural dry matter mm d 1 7 drainage daily drainage mm d 1 7 drainagesum drainage mm 7 dtranspi daily plant transpiration mm d 1 7 dwnapo daily variation of plant apoplastic substrate N pool kgN m 2 d 1 7 dwnsym daily variation of plant symplastic substrate N pool kgN m 2 d 1 7 ea vapour pressure at reference height z above the canopy kPa 7 ETR2ETO real versus potential evapotranspiration 7 ETO reference evapotranspiration mm 7 ETP potential evapotranspiration mm 7 E_ds difference
7. 30 25 27 278 15 10 6 60 19 0 0 022 5 e 3 4 0 05 1 0 225 278 15 0 610 0 592 0 570 0 574 0 590 0 609 0 64 0 035 0 035 0 015 0 05 0 041 0 39 0 435 0 5 0 422 0 20 0 20 0 52 1 6 0 095 0 297 0 238 0 145 0 195 0 030 15 22 47 22 6 33 95 1 076 0 66 0 05 i 1 1 11 23 E TextPad C PaSim code RUNS REF _pasim_sitelancien_parami0ens Bo File Edit Search View Tools Macros BE Window Help 21 OY 3 DT_ DENIT 0 00025 SOILWATERINT 0 02 VERSION 2 DENITRIF 1 INPUT_FILE RUN names_files input_oensingen txt HISTORY_VAR pasimvar txt HISTORY Output out equilibre HISTORY_NAME year tjulian wcorganic wnorganic HISTORY_WRT_FREQ 86400 HISTORY_CAIC _FREO 1728 HISTORY_CALCUL NONE NONE AVE AVE RESTART_FILE_IN NONE RESTART_ FILE_ OUT restart txt WRITE LAST_TURN SORTIE ASCII CYCLE_METEO 6 CYCLE_GESTION 6 SOMITERMIN 1 SOMITERMAX 2000 SOMERRORMAX 0 05 FLAG_EQUILIBRE 3 FLAG LAISTRESS 1 FLAG_WATERSTRESS 1 FLAG_AGESTRESS 1 FLAG_MORTAGRAZ 1 FLAG_SATURANT 0 FLAG_NONLIMITANT 0 FLAG AUTOGESTION 0 DYN_LEGUME 0 PARAM SLAM 33 5 PARAM TREP 278 0 PARAM TASUMREP 225 0 PARAM TBASE 278 0 NE_FICHIERS_ PAR 1 NE_MANAGEMENT 1 NB_POINTS_TERRE 1 NB_POINT_METEO 1 NUM_POINT_TRAVAIL 1_1 TSTOP 2191 Figure 6 Example of a run file lt 24 25 2 2 3 Steady state simulations The parameters and variables required in initial conditions file see Section 2 1 1 4 are usually not all availa
8. Graux et al 2011a b Lardy et al 2011 4 The inorganic soil N available for root uptake may be reduced through immobilization leaching ammonia volatilization and nitrification denitrification the latter processes leading to N20 emissions to the atmosphere Management includes mineral and or organic e g solid manure slurry N fertilization mowing and grazing and can either be set by the user or optimized by the model 1 2 Recent improvements PaSim was improved by Schmid et al 2001 and Riedo et al 2002 to simulate respectively N20 production and emission and the exchange of ammonia with the atmosphere Vuichard et al 2007a further developed PaSim to simulate animal herbage selection at pasture and associated enteric methane emissions They also improved the simulation of herbage biomass dynamics by accounting for the limitations induced by high leaf area index soil water deficits and aging of leaves They added a two step procedure which allowed determining the optimal stocking rate and fractional coverage of grazing at the forage system scale Since then Graux 2011 performed the model for e Vegetation i Water stress parameterization to be less influent ii plant reserve addition iii parameterization for sown Festuca arundinacea L and Lolium perenne L and permanent grasslands e Soil i N20 diffusion calculation ii surface temperature simulation a litter layer at top soil was included iii
9. VALUE Potential eating rate of lactating cows kg DM animal only used by old module version 15 Weight of lactating cows kg only used by old module version 650 Type of animal 1 dairy cows 2 suckler cows 3 old module dairy cows 4 dairy heifers 5 suckler heifers 6 sheep with old module Calving date for dairy or suckler livestock system d Useless for old module version Suckling period for suckler livestock system d Useless for old module version Age of the calves exit for suckler livestock d Useless for old module version systems Proportion of young suckler cows 3 or 4 years Useless for old module version 0 20 old or primiparous dairy cows in the cattle Calf birth Weight for suckler livestock systems kg Useless for old module version 45 Milk production at peak for young or primiparous kg animal d Useless for old module version 8 suckling 28 dairy Milk production at peak for mature or multiparous kg animal d Useless for old module version 10 suckling 34 dairy Quantity of concentrate provided per kg of milk kg DM kg of Useless for old module version 0 125 milk Concentrate energy value UF kg Useless for old module version Forage energy value UF kg Useless for old module version Forage fill value UE kg Useless for old module version N fraction in the forage kg N kg Useless for old module version 0 120 N fraction in the concentrate kg N kg Useless for old module version 0 120 Initial cow liveweight
10. animal ha of grazed land animal ha of total grasslands Figure 7 Procedure used in PaSim to optimize stocking rates and fractional coverage of cut and grazed grasslands When mowing is simulated cutting events are function of plant growth and occur every 30 or more days after 30 days of regrowth a new cut is triggered whenever plant growth rate declines during 10 consecutive days When grazing is simulated it starts when herbage dry matter intake DMI is above a fixed fraction of the potential intake VDM which reflects herbage biomass availability This fraction Kintake tolerance iS assumed to depend upon farmer s attitude to animal herbage deprivation and is therefore a parameter of the model When DMI drops below Kintake tolerance X VDMP grazing stops and animals are considered at barn To avoid numerical instability grazing resumes when DMI becomes greater than Kintake tolerance VDMI 0 1 and after a minimum 15 day delay between two consecutive periods In so doing the procedure gives the number of days when animals are at pasture Np and consequently at barn Ng Contrary to Vuichard et al 2007a who also used a two step procedure to optimize mineral N fertilization with first soil N saturation and then N fertilization limitation the latter is optimized with a one step procedure based on nitrogen nutrition index Graux 2011 Some limitations can be highlighted i As PaSim does not simulate ani
11. balwatersurf surface water balance of the system mm 7 balwatersys water balance of the system mm 7 BCScows Average BCS of cows Kg animal 1 7 BCSmature Body score condition of mature suckler cows 7 BCSyoung Body score condition of young suckler cows 7 BNF_1bnf daily biological nitrogen fixation kg N m 2 7 bnfsum biological nitrogen fixation kg N m 2 7 C carbon substrate concentration in plant kg C kg DM 1 9 c2nratioactive C N ratio of active fraction of soil organic matter kg C kg N 1 9 c2nratiopas C N ratio of pasive fraction of soil organic matter kg C kg N 1 9 c2nratioslow C N ratio of slow fraction of soil organic matter kg C kg N 1 9 caprise daily capillary rise mm d 1 7 caprisesum capillary rise mm 7 CH4young CH4 producted by Young primipare cows Kg C m d 7 CH4mature CH4 producted by Mature mulitpare cows Kg C m d 7 controle_A_S annual carbon substrate biomass kg C kg DM 1 7 Cplant total substrate and structural plant carbon kg C m 2 9 Csystem total plant and total organic soil carbon in the system kg C m 2 9 da deficit in atmospheric vapour pressure kPa 7 dah main rooting deth m 7 dETR2dETO real versus potential daily evapotranspiration mm 7 dETO daily reference evapotranspiration mm 7 dETP daily potential evapotranspiration mm 7 devapo daily soil evaporation mm d 1 7 devear Developmental stage at which ear emergence starts 7 devstage development stage index 7 dfcl
12. 1 9 rsomsum soil respiration kg C m 2 9 Rsoil Soil respiration root OM kg C m 2 9 Rsoilsum Yearly sum of soil respiration root OM kg C m 2 9 rstruct microbial respiration for decomposition of carbon in structural fraction of plant residue kg C m 2 d 1 9 rstructsum annual microbial respiration for decomposition of C in structural fraction of plant residue kg C m 2 9 runoffsum runoff mm d 1 7 rurinesum respiration associated with urine hydrolysis gives ammonium N and CO2 kg C m 2 9 sla specific leaf area m2 kg 1 7 slam Maximum specific leaf area m2 kg 1 7 snow snow at the soil surface mm 7 ssw water at the soil surface mm 7 Storage_rC Carbon labile concentration in plant kg C m 2 9 Storage_rN Nitrogen labile concentration in plant kg N m 2 7 Storage_rrC Carbon stable concentration in plant kg C m 2 9 Storage_rrN Nitrogen stable concentration in plant kg N m 2 7 s_temp slope of the saturation vapor pressure temperature curve kPa C 1 7 ta air temperature at reference height z K 7 tameani average air temperature 6 days before for the determination of the beginning of growth or not K 7 tamean2 average air temperature 5 days before for the determination of the beginning of growth or not K 7 tamean3 average air temperature 4 days before for the determination of the beginning of growth or not K 7 tamean4 average air temperature 3 days before for the determination of the beginning of growth or not K
13. A Riedo M Fuhrer J 2001 Process based modelling of nitrous oxide emissions from different nitrogen sources in mown grassland Nutr Cycl Agroecosys 60 177 187 58 Schwinning S and Parsons A J 1996 A spatially explicit population model of stoloniferous N fixing legumes in mixed pasture with grass J Ecology 84 799 813 Thornley J H M 1998 Grassland dynamics An ecosystem simulation model CAB International Wallingford United Kingdom 256p Vermorel M Jouany J P Eugene M Sauvant D Noblet J Dourmad J Y 2008 Evaluation quantitative des missions de m thane ent rique par les animaux d levage en 2007 en France INRA Productions Animales 21 403 418 Vuichard N 2005 Mod lisation des flux de gaz a effet de serre des prairies europ ennes Th se de doctorat de l Universit PARIS VI Paris France 295 pp Vuichard N Soussana J F Ciais P Viovy N Ammann C Calanca P Clifton Brown J Fuhrer J Jones M Martin C 2007a Estimating the greenhouse gas fluxes of European grasslands with a process based model 1 Model evaluation from in situ measurements Global Biogeochem Cy 21 GB1004 1 GB 1004 14 Vuichard N Ciais P Viovy N Calanca P Soussana J F 2007b Estimating the greenhouse gas fluxes of European grasslands with a process based model 2 Simulations at the continental level Global Biogeochem Cy 21 GB1005 1 GB1005 13 59 AL
14. Output_data list_of_output_variable Simulation_properties names_files_input links_to_input_files Eee NE Day int ci Day int Hour int si rss Hourly_temperature double Site_specific_parameters list_of_possible_ouput_variable restart txt file_for_run_from_equilibrium ite C02 dat Year int Site management dat Dy nt management_data Annexe 1 Usual Tree Structure of PaSim 60 Annexe 2 Example of management file PB exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage 176 227 261 216 286 500 177 241 308 178 241 297 186 255 299 187 235 Fichier Edition Format Affichage 142 182 231 153 230 500 138 183 244 137 186 259 270 303 500 93 123 Fichier Edition Format Affichage 2 Nfertamm 0 001725 0 0 000769231 0 0015 0 0015 0 0 Fichier Edition Format Affichage Nfertnit 0 001725 0 0 000769231 0 0015 0 0015 0 0 gt Ln 1 Col 1 z 61 P exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage 2 nanimal BIS 500 500 500 500 500 500 500 500 500 500 500 500 500 500 500 500 500 Pa tl r exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage 2 danimal O Ln Colt x P exemple_management_Oensingen txt Bloc notes BE Fichier Edition Format Affichage Nfertvg 0 002486828 003227081 0 0 0 005353003 0 001896733 0 0 0005057
15. PaSim model Introduction PaSim Riedo et al 1998 https www1 clermont inra fr urep modeles pasim htm is a process based grassland ecosystem model based on the Hurley Pasture Model Thornley 1998 whose main aim is to simulate climate change impacts on grassland services and feedbacks associated with GHG emissions to the atmosphere It was first programmed in ACSL Advanced Continuous Simulation Language http en wikipedia org wiki Advanced Continuous Simulation Language and developed at the Research Station Agroscope Switzerland Reckenholz from 1997 to 2002 Since then it is developed at the Grassland Ecosystem Research Unit of the French National Institute for Agricultural Research France Clermont Ferrand https www1 clermont inra fr urep The software is now written in Fortran 90 language language translation by A Cozig and contains about 60 000 lines It is composed of submodels for plants animals microclimate soil biology soil physics and management The 5 3 version of the model is about to be submitted at the APP French agency for software protection This manual aims at describing the basic structure and use of PaSim for single year multi year and steady state simulations 1 PaSim presentation 1 1 General description Grassland processes are simulated on a time step of a 1 50 of a day in order to have detailed sub daily dynamics and ensure energy budgets stability Simulations consider a soil vegetation
16. Precipitations mm d 1 IATMtot Radiation Jem RH Relative Humidity U Daily mean Wind speed m s 1 CO2 Daily mean CO atmospheric ppm concentration NH3 Daily mean NH atmospheric ppm concentration Table 1 Description of A hourly or B dail NECESSARY MODIFICATIONS PASIM needs daily weather data at each hourly time step If precipitations are in mm h 1 multiply by 24 If temperature is in Celsius degrees 273 15 add If radiation is in J cm divide by 0 36 If Relative humidity RH use Bolton 1980 Ea 0 61 12 exp 17 67 Ta Ta 243 5 RH 100 Where Ta is in C 2 could be set as default value NECESSARY MODIFICATIONS 2 could be set as default value climate variables needed to run PaSim 11 2 PaSim simulations 2 1 How to fill in files 2 1 1 Input files Input data required to run PaSim are split into 5 files for e Climate Management Site specific conditions latitude altitude soil properties etc Initial conditions for plant soil and animals Run properties options output variable list simulation length etc See the usual tree structure of PaSim in Annexe 1 As PaSim is developed in Fortran language input data must not contain coma Decimal separator must be point To separate columns you can use either space or tabulation 2 1 1 1 Weather data files 2 1 1 1 1 Hourly meteorological data PaSim needs one file for each meteorological variable Tab 1 Each of these files mus
17. carbon from system respiration t C ha 9 GWP_M global warming potential gwp of methane from animals t C ha 9 GWP_N global warming potential gwp of nitrogen from denitrification t C ha 7 hcan canopy height m 7 hcanmax Flowering plant height highest leaf not elongated m 7 HumidityIndex ratio precipitations potential evapotranspiration mm 7 h_10 threshold canopy height for light competition or umbrage effect m 7 htot total sensible heat flux W m 2 7 iatmtot global radiation 300 3000nm W m 2 7 inetc net radiation above canopy W m 2 7 68 inetcslope slope of the net radiation at the soil surface 7 inetcsum net radiation above the canopy W m 2 7 inets net radiation at soil surface W m 2 7 inetsslope slope of the net radiation above the canopy 7 inn Nitrogen Nutrition Index 7 intake_animal daily animal intake per animal kg DM animal 1 d 1 7 intake_animalsum intake per Isu kg DM animal 1 7 intake daily animal intake per m2 kg DM m 2 d 1 7 intakesum intake per m2 kg DM m 2 7 irrigation daily irrigation mm d 1 7 irrSum irrigation mm 7 ishadedpar PAR absorbed from shaded leaves in canopy W m 2 5 isunpar PAR absorbed from sunlit leaves in canopy W m 2 5 k k 5 kplantalt factor controlling the effect of altitude on shoot growth 7 kplantdev factor controlling the effect of development on shoot growth 7 kplantsht factor controlling the effect of temperature on shoot growth 7
18. dry matter kg N m 2 7 wlam1 lamina component age 1 of shoot structural dry matter kg DM m 2 9 wlam2 lamina component age 2 of shoot structural dry matter kg DM m 2 9 wlam3 lamina component age 3 of shoot structural dry matter kg DM m 2 9 wlam4 lamina component age 4 of shoot structural dry matter kg DM m 2 9 wn substrate nitrogen biomass of nitrogen substrate in plant kg N m 2 7 wnactive nitrogen in active fraction of soil organic matter kg N m 2 7 wnapo nitrogen substrate in apoplast kg N m 2 7 wnmetabolic nitrogen in metabolic fraction of plant residue kg N m 2 7 wnorganic total organic nitrogen in soil kgN m 2 7 wnpassive nitrogen in passive fraction of soil organic matter kg N m 2 7 wnslow nitrogen in slow fraction of soil organic matter kg N m 2 7 wnsym nitrogen substrate in symplast kg N m 2 7 wr root structural dry matter kg DM m 2 9 72 wri wr2 wr3 wr4 wrtot wsh wshtot wshtotsum wstl wst2 wst3 wsi4 year yieldcsum yieldnsum zsm root structural dry matter of age 1 kg DM m 2 9 root structural dry matter of age 2 kg DM m 2 9 root structural dry matter of age 3 kg DM m 2 9 root structural dry matter of age 4 kg DM m 2 9 total structural and substrate root biomass kg DM m 2 9 shoot structural dry matter kg DM m 2 9 total structural and substrate shoot biomass kg DM m 2 9 yield total substrate structural shoot dry matter kg DM m 2 9 stem component age 1 of
19. fraction of shoot structural growth partitioned to the stems kg kg 1 7 fear fraction of shoot structural growth partitioned to the ears kg kg 1 7 fn nitrogen in structural dry matter kg N kg 1 DM 7 fn2osoilatm n20 exchange between the soil and the atmosphere or daily n20 emission kg N m 2 d 1 7 67 fnaposym daily active substrate nitrogen flux from apoplast to symplast kg N m 2 d 1 7 fnatmsum nitrogen deposition kg N m 2 7 fncuticleSsum annual N from the leaf cuticle washed to the soil surface through precipitation kg N m 2 7 fnh3_ns daily ammonia flux trough stomata kg N m 2 d 1 7 fnh3_nsoil ammonia volatilization from soil kg N m 2 d 7 fnh3_nsoilsum annual ammonia volatilization from soil kg N m 2 7 fnh3_ntsum annual ammonia losses from volatilization 7 fnimmexusum immobilisation from N root exudation kg N m 2 d 1 7 fnimmminsum immobilisation from N plant residue kg N m 2 d 1 7 fnmintot N soil mineralization kg N m 2 d 1 7 fnmintotsum annual N soil mineralization kg N m 2 7 fnref parameter controlling nitrogen concentration of structural dry matter kg N kg 1 7 fnresidue nitrogen in flow of plant residue kg N m 2 d 1 7 froot Relative root dry matter in different soil layers 2 fnsymapo daily nitrogen diffusion between apoplast and symplast kg N m 2 d 1 7 fresidue Flow of plant residus kg DM m 2 7 ftclover target legume fraction 7 fwroot factor controlling the effect of soil water con
20. grazingc C flux associated to grazing kg C m 2 d 1 9 grazingestT structural carbon lost by grazing kg C m 2 9 grazingcsum C in yearly grazed plant dry matter kg C m 2 y 1 9 grazingear1 biomass of ear compartement age 1 grazed by animals kg DM m 2 9 grazingear2 biomass of ear compartement age 2 grazed by animals kg DM m 2 9 grazingear3 biomass of ear compartement age 3 grazed by animals kg DM m 2 9 grazingear4 biomass of ear compartement age 4 grazed by animals kg DM m 2 9 grazinglami biomass of lam compartement age 1 grazed by animals kg DM m 2 9 grazinglam2 biomass of lam compartement age 2 grazed by animals kg DM m 2 9 grazinglam3 biomass of lam compartement age 3 grazed by animals kg DM m 2 9 grazinglam4 biomass of lam compartement age 4 grazed by animals kg DM m 2 9 grazingnstT structural nitrogen lost by grazing kg N m 2 7 grazingstem1 biomass of stem compartement age 1 grazed by animals kg DM m 2 9 grazingstem2 biomass of stem compartement age 2 grazed by animals kg DM m 2 9 grazingstem3 biomass of stem compartement age 3 grazed by animals kg DM m 2 9 grazingstem4 biomass of stem compartement age 4 grazed by animals kg DM m 2 9 grazingwc carbon substrate lost by grazing kg C m 2 9 grazingwn nitrogen substrate lost by grazing kg N m 2 7 gs soil heat flux W m 2 7 gsh shoot growth rate kg m 2 d 1 9 gsslope soil heat flux taking into account slope W m 2 7 GWP_C global warming potential gwp of
21. matter kg Nika 0 022 Name 3 Relative root dry matter in different soil layers Shoot dry matter after cutting kg m LAI after cutting m leaf m2 Figure 9 Plant tab of the graphical interface This tab contains all the plant parameters of the grassland The canopy height parameter cannot be changed in the interface 40 VARIABLE UNIT HELP ADVISE D VALUE Cumulated depth of soil layers mm First layer must be 20 mm Cumulated depth of lower soil boundary mm Must be larger than previous soil layer layer Bulk density of each soil layer kg L All the same or increasing values Sand fraction of texture Clay fraction of texture Silt fraction of texture Saturated soil water content m m could be estimated thanks to the following formula 1 dendity 2 65 Saturated soil water content of lower m m Same as last layer boundary layer Air entry potential mm Use soil routine Air entry potential of lower soil boundary mm Same as last layer layer Parameter b in psi Use soil routine Parameter b of lower soil boundary Same as last layer layer Saturated hydraulic conductivity mmd Use soil routine Saturated hydraulic conductivity of mmd NOT USED ANYMORE lower soil boundary layer Parameter for the determination of the NOT USED ANYMORE 0 01 field capacity Field capacity m m Use soil routine Permanent wilting point m m Use soil routine Soil pH 7
22. paths e g names files input_sitel_yeart_ graz txt The management file for automatic grazing e g site yeari management_graz dat must have the following information still 180 columns tcut 500 500 500 500 500 500 500 500 500 500 tfert 500 500 500 500 500 500 500 500 500 500 Nfertamm 0000000000 Nfertnit 0000000000 Nanimal 0000000000 tanimal 500 500 500 500 500 500 500 500 500 500 danimal 0000000000 Nliqmanure 0000000000 Nslurry 0000000000 Nsolmanure 0000000000 LW Ycows 0000000000 LWMcows 0000000000 BCSYcows 0000000000 BCSMcows 0000000000 LWcalves 0000000000 AGE_cow_P 0000000000 AGE_cow_M 0000000000 Forage quantity 0000000000 32 33 The specific file for the input data file paths e g names files input_sitel_year1_graz txt must have the following form Input conditions site1_ site_spe par Input conditions site1 init_cond par Input conditions site1_year1 management_graz dat Input meteo Ta dat Input meteo ea dat Input meteo u dat Input meteo IATMtot dat Input meteo Pa dat Input meteo NH3 dat Input meteo CO2 dat Input conditions site1_year1 management_cut_yield_inn dat 2 In the PaSim run file you have activate e FLAG_FERTILIZATION 1 e FLAG AUTOGESTION 2 e RESTART FILE IN restart txt e RESTART FILE OUT restart_site1_year1_graz txt and to specify the path of the names _ files input_sitel_year1_graz txt file This simulation lasts more than a single year simulation a
23. shoot structural dry matter in second age component stem shoot structural dry matter in third age component C14 or C13 fraction in stem shoot structural dry matter in third age component stem shoot structural dry matter in fourth age component C14 or C13 fraction in stem shoot structural dry matter in fourth age component lamina leaf area index in first age component lamina leaf area index in second age component lamina leaf area index in third age component lamina leaf area index in fourth age component stem leaf area index in first age component stem leaf area index in second age component stem leaf area index in third age component stem leaf area index in fourth age component Temperature in soil layer 1 Temperature in soil layer 2 Temperature in soil layer 3 Temperature in soil layer 4 Temperature in soil layer 5 Temperature in soil layer 6 Soil surface liquid water Snow cover Volumetric water content in soil layer 1 Volumetric water content in soil layer 2 Volumetric water content in soil layer 3 Volumetric water content in soil layer 4 Volumetric water content in soil layer 5 Volumetric water content in soil layer 6 Bq kg kg m Bq kg kg m Bq kg kg m Bq kg kg m Bq kg kg m Ba kg kg m Bq kg kg m Bq kg kg m Bq kg kg m Bq kg kg m Bq kg kg m Bq kg m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 m2 88 89 90 91 92 93 94 95 96 97 9
24. supplementation 4 Automatic supplementation forage and concentrate for suckler and dairy cattle respectively FLAG_DIFF 0 old way to calculate N20 diffusion Due to computation time prefer use old 1 1 activate N O diffusion calculated by Crank Nicolson method during equilibrium research and method Crank Nicolson method for other simulations FLAG_EQUILIBRE 0 No equilibrium research 1 Iterative method of SOM equilibrium 3 Algebraic method of SOM equilibrium SOMITERMIN Minimum number of steps required to reach SOM 1 equilibrium with climate and management SOMITERMAX Maximum number of steps required to reach SOM 1000 equilibrium with climate and management Table 5 Description of information needed in the run file 21 2 1 3 PASIM run file This file contains the different modalities of simulation e basic time step calculation modalities for SOM equilibrium output variables options of simulation automatic management specific parameters for vegetation spatialization The order of the lines does not matter and most of the parameters or options have advised values in code if they are not in PaSim file To know the list of possible output variables you can refer to the pasimvar file Annexe 3 2 2 How to run PaSim 2 2 1 General settings and standard single year simulations Before PaSim can be run it is necessary to make sure that all necessary files exist and have been defined for your own simulation A
25. 0 1 39145964 1135 119 0 460 0 0 0 em 4 98221E 4 154 8 0 i h 0 0 B S4093E 4 162 3 0 4 98221E 4 165 19 0 Nanimal Tanimal ot AGE_cO AGE_CO 6 40569E 4 mn es Nanimal Danimal AGE co to AGE_co on Forage m 4 62633E 4 14 0 E A i 0 0 5 33808E 4 a 0 0 i 0 0 13 55872E 4 20285E 4 2 4911E 4 Nanimal i LWYcows AGE_co AGE_co 388 0 58 Figure 13 Animal tab of the graphical interface Global animal properties are defined in the first array In the following arrays 1 array per year the user defines the animal management he can use up to 10 lines for 10 events button to add or delete lines 48 49 3 7 The outputs tab EB PaSim Laqueuille_ int File Run Results Mode 7 7 j Te p Overview Plant Soil Meteo Cut amp Fert Animal OutPuts Properties Datas Choose a list OutPuts Displayed Graph NONE MMe e RR RR RRR RRR RRR RRR IK IS IK IK IR IK ISIS ISIS ISIS ile Figure 14 Outputs tab of the graphical interface In this tab the user can choose all the variables he wants in output for PaSim run He can also choose if he wants graphics of these variables or not The annexe 3 is listing the variables The interface also proposed to load a pre defined list of variables corresponding to the most asked variables
26. 0 Initial condition for soil water content m m not higher than saturated value Capillary rise from lower boundary 3 layer yes 1 0 or no 0 0 Water content of lower soil boundary m m Should not be higher than layer in spring saturated value Water content of lower soil boundary m m Should not be higher than layer in autumn saturated value Phase of temperature of lower soil rad boundary layer calculated by of the soil routine of Pierluigi Calanca Table 7 the soil tab parameters 41 3 3 The soil tab PaSim Laqueuille_int File Run Results Mode rn at Overview Plant Soil meteo Cut amp Fert Animal OutPuts Properties Name Depth of soil layers mm Cumulated depth of lower soil boundary layer mm Bulk density of each soil layer kal Sand fraction of texture ra 3 Clay fraction of texture 1G Silt Fraction of texture E Saturated s soil water content mama ae Sat soil water cont of lower boundary layer m3 m3 Air entry potential mm Air entry potential of lower soil boundary layer mm Parameter b in psi Parameter b of lower soil boundary layer Saturated hydraulic conductivity mmjd Saturated hydraulic conductivity of lower sol ry layer mm d Field capacity calculated by of the soil routine Pierluigi m3 m3 Permanent wilting point calculated by the soil routine of Pierluig mama Soil pH Initial con
27. 0 050 589 126 13 908 24 995 0 530 en 0 100 589 126 13 908 24 995 0 530 ec 0 300 631 338 14 541 21 773 0 460 0 510 665 724 15 010 19 583 0 460 0 700 654 967 14 794 20 220 0 460 Figure 2 Description of soil routine utilization 3 Soil output exemple txt Qfe Qpw m3 m3 m3 m3 0 468 D 355 0 468 D 355 0 468 D 355 0 410 D 315 0 413 D 320 0 412 0 318 13 NB When using daily meteorological data you have to repeat 7 times the path of the daily meteorological data file in the name_files_input file For instance Input condition oens site_spe par Input condition oens init_cond par Input condition oens management dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Input meteo oens Daily_meteo dat Just the daily temperature and radiation are interpolated into hourly weather data other variables remain constant during the day Their interpolation is based on equations from Grassland dynamics an ecosystem simulation model Thornley 1998 p 146 150 2 1 1 2 Management file For each type of agricultural practice mowing grazing N fertilization PaSim user can fulfil up to 10 events per year When less than 10 values of the date of an event e g cutting event are available put a number greater than 366 e g 500 Data must
28. 1 9 ranimal daily animal respiration kg C m 2 d 1 9 ranimalsum annual animal respiration kg C m 2 9 rb bulk blattgrenzschichtwiderstand s m 7 rbelowplantS total plant respiration for root growth and maintenance at steady state kg C m 2 d 1 9 rc bulk stomatal resistance the canopy s m 7 RECO Ecosystem respiration kg C m 2 9 regcount counter of cuts 7 rexudation microbial respiration of exudates from root respiration kg C m 2 d 1 9 rgr growth respiration of root kg C m 2 d 1 9 rgsh growth respiration of shoot kg C m 2 d 1 9 rmetabolic microbial respiration for decomposition of carbon in metabolic fraction of plant residue kg C m 2 d 1 9 rmr outputs of substrate C for root maintenance kg C m 2 d 1 9 rmsh outputs of substrate C for shoot maintenance kg C m 2 d 1 9 rn respiration associated with root n uptake kg C m 2 d 1 9 root_density root_density 2 Roots_psiw weighted mean of the soil water potentials in the different soil layers 7 rpassive microbial respiration for decomposition of C in passive fraction of soil organic matter kg C m 2 d 1 9 rplant daily plant respiration kg C m 2 d 1 9 rplantsum plant respiration at steady state kg C m 2 9 rs soil surface resistance s m 7 rsa aerodynamic resistance between soil surface and canopy source height s m 7 rslow microbial respiration for decomposition of C in slow fraction of soil organic matter kg C m 2 d 1 9 rsom daily soil respiration kg C m 2 d
29. 26 gmean 8 Average growth rate during regrowth for plant layer 8 kg m d 127 gmean 9 Average growth rate during regrowth for plant layer 9 kg m d 128 gmean 10 Average growth rate during regrowth for plant layer 10 kg m d 129 nfertammundissolved_inter Total ammonium dissolved from first time step Kg N m 130 nfertnitundissolved_inter Total nitrate dissolved from first time step Kg N m 131 kt1 Thermal conductivity of layer 1 Int r t W m K 132 kt2 Thermal conductivity of layer 2 W m K 133 kt3 Thermal conductivity of layer 3 W m K 134 kt4 Thermal conductivity of layer 4 W m K 135 kt5 Thermal conductivity of layer 5 W m K 136 kt6 Thermal conductivity of layer 6 W m K 137 tsoilom Average temperature of lower boundary layer K 138 lecs 1 Water extracted by the root for the layer 1 mm 139 lecs 2 Water extracted by the root for the layer 2 mm 140 lecs 3 Water extracted by the root for the layer 3 mm 141 lecs 4 Water extracted by the root for the layer 4 mm 142 lecs 5 Water extracted by the root for the layer 5 mm 143 lecs 6 Water extracted by the root for the layer 6 mm 144 Storage_rC Carbon labile conentration in plant kg C m2 145 Storage_rrC Carbon stable conentration in plant kg C m2 146 Storage_rN Nitrogen labile conentration in plant kg N m2 147 Storage _rrN Nitrogen stable conentration in plant kg N m2 76 Annexe 5 restart file of PaSim restart txt C version If you wish to modify the restart file manually take care to the
30. 50 51 3 8 The properties tab EAST Laqueuille_int File Run Results Mode Overview Plant Sail Meteo Cut amp Fert Animal OutPuts Properties TSTART 1 TSTOP nb of years El v 2921 Generate the pasim file INPUT_FILE RUN names_files_input_lag int txt CYCLE_METEO 8 i CYCLE_GESTION DT DT_DENIT Valid SOILWATERINT HISTORY fOutput out Laqueuille_int HISTORY_YAR Jpasimvar Ext HISTORY_NAME year Ejulian bnfsum c Cplant devstage fclover gr gcrsum gsh geshsum hcan intake lai MethaneSum n n2oemissionsum Nplan HISTORY_WRT_FREQ 86400 HISTORY_CALC_FREQ 1728 HISTORY_CALCUL NONE NONE NONE AVE AVE AVE AVE AVE NONE AVE NONE AVE AVE AVE NONE AVE AVE AVE AVE AVE AVE AVE NONE NO WRITE AL gt SORTIE asc 9 DENITRIF MV FLAG_LATSTRESS V FLAG_WATERSTRESS V FLAG AGESTRESS W FLAG_MORTAGRAZ C FLAG_PLOUGHING DFLAGIRRIGATION FLAG_FERTILIZATI U FLAG_AUTOGESTION 7 FLAG_SATURANT CI FLAG_NONLIMITANT FLAG_DIFF DYN_LEGUME CI FLAG_ROOT_PROF FLAG_ISOTOPE c12 0 FLAG_EQUILIBRE None 0 vi SOMITERMIN 1 SOMITERMAX 1000 SOMERRORMAX 0 1 RESTART_FILE_IN U NONE or Choose the RESTART_FILE OUT None or C PARAM_FCLOVER PARAM_FROOT 1 2 3 4 5 6 0 145 0 398 0 248 0 164 0 041 p oo4o Figure 15 Properties tab of the graphical interface In this interface the user can see and modify all the variables presents in the
31. 7 tamean5 average air temperature 2 days before for the determination of the beginning of growth or not K 7 tamean6 average air temperature 1 day before for the determination of the beginning of growth or not K 7 tameand mean air temperature 7 tasum air temperature sum k d 7 tasumrep Normalization factor for development Menzi 1998 C d 7 tasumd cumulated units of plant development or efficient temperature sum Kd 7 tgrowth date of beginning of plant growth after last cut d 7 thetas volumetric water content in soil layer h m3 m 3 2 thetas_1 soil water content of first soil layer m3 m 3 7 thetas_2 soil water content of second soil layer m3 m 3 7 thetas_3 soil water content of third soil layer m3 m 3 7 thetas_4 soil water content of fourth soil layer m3 m 3 7 thetas_5 soil water content of fifth soil layer m3 m 3 7 thetas_6 soil water content of sixth layer m3 m 3 7 tjulian julian day d 8 tleaf leaf temperature K 7 transpisum plant transpiration mm 7 71 tsoil soil layer temperature k 2 tsoil_1 soil temperature of layer 1 K 7 tsoil_2 soil temperature of layer 2 K 7 tsoil_3 soil temperature of layer 3 K 7 tsoil_4 soil temperature of layer 4 K 7 tsoil_5 soil temperature of layer 5 K 7 tsoil_6 soil temperature of layer 6 K 7 tsoilcumm cumulated mean soil temperature k 7 tss soil surface temperature k 7 tss0 value for testing tss 8 tssOdiff value for testing tss 8 tssdiff value for
32. 8 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 nfertammundissolved nfertnitundissolved nno2 1 nno2 2 nno2 3 nno2 4 nno2 5 nno2 6 nn2odenit 1 nn2odenit 2 nn2odenit 3 nn2odenit 4 nn2odenit 5 nn2odenit 6 snowfallsum lessum lecsum freezingsum snowmeltsum rainsum snowfallsumprev lessumprev freezingsumprev snowmeltsumprev rainsumprev wr wr1_C14 wr2 wr2_C14 wr3 wr3_C14 wr4 wr4_C14 regcount devstage tameani tamean2 tamean3 tamean4 tamean5 tamean6 tameand tacumm tacummprev tasumd tcutO tayearsum hsteadystate nanimaltot nfertammtot nfertnittot fertcount Ammonium from mineral fertilisation undissolved Nitrate from mineral fertilisation undissolved NO in soil layer 1 NO in soil layer 2 NO in soil layer 3 NO in soil layer 4 NO in soil layer 5 NO in soil layer 6 N20 content in the denitrification pool of soil layer 1 N20 content in the denitrification pool of soil layer 2 N30 content in the denitrification pool of soil layer 3 N20 content in the denitrification pool of soil layer 4 N30 content in the denitrification pool of soil layer 5 N20 content in the denitrification pool of soil layer 6 Yearly sum of snow fall Sum of soil evaporation Sum of plant transpiration Frozen water Slush Yearly sum of rain fall Does not
33. 96 0 0 0 0 Q 0 00127 0 00463 wall Uni Coli a 00184 0030135 62 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage 2 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage NFertmist O DB exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage Uni Coll Lw of young cows 0 0 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage Lw of mature cows O 0 0 TEE 63 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage BCS of young cows 0 Q 0 Ln 1 Col 1 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage BCS of mature cows Ln 1 Col 1 DB exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage Initial calf Lw Cat the beginning of grazing period 0 0 0 0 0 Ln 1 Col 1 exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage Intial age cow Primi 36 36 36 a Ini Colt at 64 PB exemple_management_Oensingen txt Bloc notes Fichier Edition Format Affichage Initial age cow multi 0 50 50 U oens management Bloc notes Fichier Edition Format Affichage Forage quantity O 0 gt O OODD DOODOODODO DOOOOO000 DOODODOODODO oooO OOOO0000 DODOODODOOODO DOOOOO0O00O0 65 Annex
34. AIL Criteria to stop SOM equilibrium search Name of the restart file obtained at SOM equilibrium and which will initialize the model instead of the initial condition input file Name of the restart file obtained after running the model to reach SOM equilibrium and which will initialized the model instead of condition input file file Maximum specific leaf area m kg Parameter for the calculation of plant development Legume fraction Specific lamina area constant kg kg C 1 Specific stem and sheaths area m2 kg 1 Michaelis Menten constant for the legume fraction calculation kgC kgN parameter controlling nitrogen concentration of structural dry matter kg N kg Parameter for the calculation of water conductivity between root and shoot kg water kg dry matter J kg water 1 d 1 canopy height parameter Root activity parameter kg N kg 1 d 1 Tillage Frequency year 1 0 lt f tillage lt 1 Normalization factor for development Kd Basal temperature for plant growth K Fraction of fibres in the total ear ingested Fraction of fibres in the total lam ingested Fraction of fibres in the total stem and sheaths ingested Flowering plant height highest leaf not elongated m Maximum of the total nitrogen concentration in plant kg N kg Rate parameter for root turnover at 20 C d Rate parameter for shoot turnover at 20 C d Fractional C content of shoot structural dry matter kg C kg
35. E sauvegardes RUNS CARBOEUROPE RUN Oensingen_int RUN names_files_input_oensingen t lt gt TOR amp Fichier Edition Recherche Affichage Outils Macros Configuration Fen tre Aide a x Dek PBSRE Bello cleazl2qlOy RELA ico Input condition oens site_spe par Input condition oens init_cond par Input condition oens_int management dat Input meteo oens Ta dat Input meteo oens ea dat Input meteo oens u dat Input meteo oens IATMtot dat Input meteo oens Pa dat Input meteo oens NH3 dat Input meteo oens CO2 dat Figure 5 Example of a names input file 20 A First part ADVISED PARAMETER DESCRIPTION HELP VALUE TSTART Beginning of the simulation Julian day 01 for the simulation to begin the 1 of 01 January of the first year TSTOP End of the simulation Julian day 365 for the simulation to stop the 31 December of the first year INPUT_FILE Path of the names input file CYCLE_METEO Number of meteorological cycles CYCLE_GESTION Number of management cycles Same annual management can be repeated several years DT Time step of most of PaSim processes day Keep 0 02 0 02 DT_DENIT Time step for denitrification processes day Keep 0 00025 0 00025 SOILWATERINT Time step for water processes percolation day Keep 0 02 0 02 FLAG_READ_METEO When activated meteorological data must be daily data Must be 1 to use daily meteorological data 0 see 4 1 for more details HISTORY_VAR Path of
36. N m d kg DM animal Kg I QAO kg kg animal d kg DM kg of milk UF kg UF kg UE kg kg N kg kg N kg kg months HELP 10 values 10 values Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Prefer default value Should not be higher than saturated value Should not be higher than saturated value Should not be higher than saturated value Is now estimated by the model So use default value Is now estimated by the model So use default value Prefer default value Prefer default value 0 only used by old module only used by old module 1 dairy cows 2 suckler cows 3 old module version dairy cows 4 dairy heifers 5 suckler heifers 6 sheep with old module Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Useless for old module version Only used for automatic management Only used for automatic management Only used for automatic management Table 4 Descript
37. PaSim User s guide Grassland Ecosystem Research Unit French National Institute for Agricultural Research December 2012 PaSim v5 3 IDDN FR 001 220024 000 R P 2012 000 10000 This document has been written by A I Graux R Lardy M Gaurut E Duclos and K Klump Table of Content 1 PaSim presentation nennen 4 1 1 General SS CMON gin are tee ee tates te nee 4 1 2 AGcentimpfioeve mensa ellenica 6 1 3 Model evaluation kn ee nn 8 1 4 Validity domain here 8 1 5 Modelling limitations acer 8 1 6 Model stengtis scrasa ene REAREA 10 li AN OMIS a cr cos 10 2 e LI ARR O rte nn OA 12 2 1 HOW to IM alla 12 2AA cloni 12 2 1 1 1 Weather data files 12 2 1 1 2 Management file 14 2 1 1 3 Site speclielle ensure 16 2 1 1 4 Initial conditions leale 18 212 Names input file eee ee ee ey ee nee ne er ner ery ares 20 2 1 3 PASIM run file aaa 22 22 HOW to r m PAS 22 2 2 1 General settings and standard single year simulations 22 2 2 2 Multi year simulations ooooonnnnnccccnnnnnnnncncnnnnccnnnccnnnnnnnnnnnnnncncnnnnnnnnnnnnns 22 2 2 3 Steady state simulations nn 26 2 3 Specific PaSim simulations ana cod 26 2 3 1 Optimal grazing coverage and stocking rate 26 2 3 1 1 HOW does it work essen iii 26 2 3 2 Howto run the procedure for optimal grazing coverage and stocking rate 30 2 3 3 Modelling C and C cycles with PaSim oocococococicicocococon
38. SOM equilibrium a new algebraic method was developed Lardy et al 2011 e Grazing animals In order to improve the accuracy of animal performance simulation during grazing we developed a new version of the animal module of PaSim In this version three animal classes can be simulated Graux et al 2011 suckler cows and their calves dairy cows and heifers only one class of cattle can be simulated within the same simulation i With suckler cows animal growth and production are described following the SEBIEN model see Jouven et al 2008 except for selective intake of sward structural components ii With heifers and with dairy cows a new mechanistic model consistent with SEBIEN was developed to simulate intake growth and with dairy cows lactation iii Simulation of enteric CH emissions is now based on Vermorel et al 2008 iv Temperature effects on forage digestibility and ingestibility are simulated v A new module was developed to simulate dairy cows supplementation by roughage and or concentrate feed e Management i Acceleration of SOM mineralization due to tillage for sown grasslands ii irrigation and N fertilization automatic management based on water stress and nitrogen nutrition indexes PaSim has also been improved in collaboration with IRSN the French nstitut de radioprotection et de s ret nucl aire to simulate C and C cycles E Duclos ISIMA training period to assess radioacti
39. _TRAVAIL Generate the parameters 57 4 References Bolton D 1980 The Computation of the Equivalent Potential Temperature Monthly Weather Review vol 108 p1046 1053 Calanca P Vuichard N Campbell C Viovy N Cozic A Fuhrer J Soussana J F 2007 Simulating the fluxes of CO2 and N20 in European grasslands with the Pasture Simulation Model PaSim Agriculture Ecosystems amp Environment Volume 121 Issues 1 2 The Greenhouse Gas Balance of Grasslands in Europe 164 174 Graux A I 2011 Modeling climate change impacts on grassland ecosystems Adaptation strategies for forage production systems Blaise Pascal University Ph D thesis 535 p Graux A I Bellocchi G Lardy R Soussana J F 2011a Ensemble modelling of climate change risks and opportunities for managed grasslands in France In revision for publication in Agriculture and Forest Meteorology Graux A I Gaurut M Agabriel J Baumont R Delagarde R Delaby L and Soussana J F 2011b Development of the Pasture Simulation Model for assessing livestock production under climate change Agriculture Ecosystems and Environment accepted Jouven M Agabriel J and Baumont R 2008 A model predicting the seasonal dynamics of intake and production for suckler cows and their calves fed indoors or at pasture Animal Feed Sci Tech 143 256 279 R Lardy G Bellocchi J F Soussana 2011 A new method to determine
40. action of plant residue Nitrogen in active fraction of plant residue Carbon in structural fraction of plant residue Nitrogen in leaf cuticle Carbon in metabolic fraction of plant residue Nitrogen in metabolic fraction of plant residue Carbon in slow fraction of plant residue Nitrogen in slow fraction of plant residue Carbon in passive fraction of plant residue Nitrogen in passive fraction of plant residue Carbon substrate in plant biomass of nitrogen substrate in apoplast biomass of nitrogen substrate in symplast Nitrogen in structural dry matter lamina shoot structural dry matter in first age component lamina shoot structural dry matter in second age component lamina shoot structural dry matter in third age component lamina shoot structural dry matter in fourth age component ear shoot structural dry matter in first age component ear shoot structural dry matter in second age component ear shoot structural dry matter in third age component ear shoot structural dry matter in fourth age component stem shoot structural dry matter in first age component stem shoot structural dry matter in second age component stem shoot structural dry matter in third age component Unites kg C m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg C m kg N m kg C m kg N m kg N m kg C m kg C m kg N m kg C m kg N m k
41. animal atmosphere system with state variables expressed per m and run over one or several years Animal processes are simulated at pasture but not in the barn As with other advanced biogeochemical models PaSim simulates water carbon C and nitrogen N cycles Photosynthetic C is allocated dynamically to root and shoot compartments and can be lost from the modelled system through ecosystem respiration animal milking and enteric CH emissions Vegetation is assumed to consist of one root and of three shoot compartments laminae sheaths and stems ears each of which is further divided into four age classes Biological N fixation is modelled according to Schwinning and Parsons 1996 when assuming a constant legume fraction Vegetation is parameterized for a set of key functional traits such as the maximum specific leaf area the light saturated leaf photosynthetic rate in standard conditions the fraction of fibres in ingested shoot compartments and the fraction of digestible fibres in total ingested fibres Accumulated aboveground biomass can be utilized by cutting and grazing or enters a litter pool The N cycle considers three types of N inputs to the soil via atmospheric N deposition fertilizer N addition symbiotic N fixation by legumes and animal faeces and urine 1 PaSim litt rature Riedo et al 1998 1999 2000 2001 2002 Schmid et al 2001 Vuichard 2005 Vuichard et al 2007a b Calanca et al 2007 Graux 2011
42. be fulfilled in a specific order Tab 2 The first line of the management file is just for user it is usually a simple remind of the different variables For example the first line can be tcut tfert Nfertamm Nfertnit nanimal tanimal danimal Nliqmanure Nslurry Nsolmanure LW of young cows LW of mature cows BCS of young cows BCS of mature cows Initial calf LW at the beginning of grazing period Initial age of primiparous cows Initial age of muliparous cows Forage quantity Each of the next lines represent one year of management and must contain 18 times 10 values of variables See Annexe 2 for example of management file Model inputs for animals are for both dairy and suckling systems i the grazing periods maximum 10 and the corresponding stocking rates ii the calving date iii the average maximum milk production at peak of lactation iv the initial average liveweight and body condition score of cows at each new grazing period The old animal module Type of animal 3 only uses the 10 first management variables 100 columns but the 180 columns still need to be present in the file NB If you have no information about inorganic fertilizer note you can consider that it is a 50 50 mixture of ammonium nitrate 3 Whenever the stocking rate is changing PaSim considers that a new grazing period is beginning 14 VARIABLE Description Latitude N exemple 55 52 20 Time of the hig
43. between saturation vapor pressure and air vapor pressure kPa 7 E_lecslope energy flux associated with transpiration W m 2 7 E les latent heat flux W m 2 7 E_leslope latent heat flux taking into account slope W m 2 7 E_lesslope energy flux associated with soil evaporation taking into account slope W m 2 7 E ts Temp rature la hauteur du couvert 7 evaposum annual soil evaporation mm 7 evapotrans evapotranspiration transpisum evaposum mm 7 exudation carbon susbtrate lost by exudation kg C m 2 d 1 9 faecesc carbon in faeces kg c m 2 d 9 faecescsum annual carbon in faeces kg C m 2 9 faecesn nitrogen in faeces kg C m 2 d 1 7 faecesnsum annual nitrogen in faeces kg N m 2 7 fcloss carbon in yield loss kg C m 2 d 1 9 fclover legume clover fraction in canopy kg kg 1 7 femetabolic decomposition rate of SOM metabolic pool kg C m 2 d 1 9 fer fractional C content of root structural dry matter kg C kg 1 7 fcrecr C substrate input from recycling of senescing root kg C m 2 d 1 9 fcrecsh C substrate input from recycling of senescing shoot kg C m 2 d 1 9 fcrecsum C substrate input from recycling of senescing dry matter kg C m 2 9 fnrecsum N substrate input from recycling of senescing dry matter kg N m 2 7 fcresidue carbon in flow of plant residue kg C m 2 d 1 9 fesh fractional C content of shoot structural dry matter kg C kg 1 7 flam fraction of shoot structural growth partitioned to the lamina kg kg 1 7 fstem
44. ble Among others getting information about the C and N content in the different soil pools is very difficult To overcome this difficulty it is possible to let PaSim generate equilibrium values of these parameters and variables through a so called steady state simulation The basic steps to run a steady state simulation are the same as for a standard simulation the only difference being in the settings of certain parameters in the PaSim run file see Section 2 1 3 e FLAG_EQUILIBRE 1 or FLAG_EQUILIBRE 3 to use either iterative or matrix method e RESTART_FILE_IN NONE e RESTART_FILE_OUT Restart txt for instance e CYCLE METEO the number of years to be simulated e g CYCLE_METEO 3 means that SOM equilibrium would be searched for 3 ar of the time series SOMERRORMAX termination criterium i e the tolerated error when reaching C and N balance steady states expressed in percent of the considered balance e SOMITERMIN minimum number of iterations e SOMITERMAX maximum number of iterations e TSTART Specify the first day of the time series on which SOM steady state will be searched for e g 366 to start at the second year of the series e TSTOP his value has no importance when searching for equilibrium 2 3 Specific PaSim simulations 2 3 1 Optimal grazing coverage and stocking rate 2 3 1 1 How does it work Vuichard et al 2007a developed a two step procedure to assess the optimal fractional coverage of grazing and the assoc
45. ch soil layer as input Cf soil input exemple txt Then the PaSim user has to run estimate soil parameters exe and the routine creates 2 output files see Figure 2 a test layer file a soil output file This routine as also been implemented into the interface The soil tab p 42 oens site_spe par 0 Description 0 825 Latitude N rad 12 3 Time of the highest position of the sun h min 0 Slope rad 0 Aspect rad 450 Height above sea level n 1 5 Micromet reference height above soil surface mm 1 5 NH3 reference height above soil surface m 6 Number of soil layers max 6 20 100 200 400 700 1000 Depth of soil layers mm 500 Depth of lower soil boundary layer mm 4 25 306 0 303 0 251 0 125 0 014 0 001 25 1 I 1 15 1 15 0 0 0 24 0 24 43 0 43 0 43 0 43 0 43 0 43 0 0 0 33 0 33 0 0 0 56 0 56 oooooHrooownor m n HW H n 410 410 410 410 410 410 410 11 15 11 15 11 15 11 5 11 5 11 5 11 5 51 5 51 5 51 5 51 5 51 5 51 5 1 5 01 464 0 464 0 464 0 0 464 0 464 0 464 0 329 0 329 0 329 6 1 0 329 0 329 0 329 076 1 076 1 076 0 66 0 66 Maximal canopy height m Canopy height parameter Clover fraction kg kg Relative root dry matter in different soil layers Main rooting depth m Bulk density kg l Volume fraction of quartz in soil m3 m3 Clay fraction of texture Silt fraction of texture Saturated soil water content
46. contain anything anymore Yearly sum of snow fall from previous time step Sum of soil evaporation from previous time step Frozen water at previous time step Slush at previous time Yearly sum of rain fall at previous time step Does not contain anything anymore root structural dry matter of age 1 C14 or C13 quantity in root structural dry matter of age 1 root structural dry matter of age 2 C14 or C13 quantity in root structural dry matter of age 2 root structural dry matter of age 3 C14 or C13 quantity in root structural dry matter of age 3 root structural dry matter of age 4 C14 or C13 quantity in root structural dry matter of age 4 counter for number of regrowths Development stage Average air temperature 6 days before Average air temperature 5 days before Average air temperature 4 days before Average air temperature 3 days before Average air temperature 2 days before Average air temperature 1 day before Average air temperature Sum of daily average temperature Sum of daily average temperature for previous day Sum of efficient temperature Julian day for first cut Yearly air sum temperature Number of meteo cycle when searching for equilibrium Stocking rate Total ammonium fertilisation with previous year Total nitrate fertilisation with previous year Counter for fertilisation application AAAAAXRAXAA o Be D lt A animal m2 Kg N m Kg N m 79 142 gmean 1 Average growth rate during regro
47. dition For soil water content m3 m3 Capillary rise From lower boundary layer yes 1 0 or no fl 0 0 E Water content of lower soil boundary layer in spring m3 m3 Water content of lower soil boundary layer i in autumn maf m3 Phase of temperature of lower soil boundary layer rad Estimate parameters Figure 10 Soil tab of the graphical interface In this tab there are all the soil parameters of the grassland Some of these can t be changed such as the depth of the first soil layer which has to be 20 millimetres The user can estimate parameters such as the air entry potential or the parameter b in psi using other parameters such as fractions of sand silt and clay After that he can choose to report or not the new values into the interface 42 Hourly Data VARIABLE Pa Ta U IATMtot Ea C13 C14 CO2 NH3 DESCRIPTION Precipitations Average air temperature Wind speed Radiation Water vapour pressure cr concentration ca concentration CO concentration NH3 concentration atmospheric atmospheric atmospheric atmospheric UNIT mm d 1 Bq kg C ppm ppm NECESSARY MODIFICATIONS PASIM needs daily weather data at each hourly time step If precipitations are in mm h 1 multiply by 24 If temperature is in Celsius degrees 273 15 add If radiation is in J cm divide by 0 36 If Relative humid
48. dry matter lost by cuts kg C m 2 9 losscsum annual carbon lost kg c m 2 9 lossn nitrogen in dry matter lost by cuts kg N m 2 7 Ist1 stem component age 1 of leaf area index m2 m 2 7 Ist2 stem component age 2 of leaf area index m2 m 2 7 Ist3 stem component age 3 of leaf area index m2 m 2 7 Ist4 stem component age 4 of leaf area index m2 m 2 7 methane daily methane emissions by herbivorous kg C m 2 d 1 9 methane_ani daily enteric methane emissions per animal kg C animal 1 d 1 9 methane_aniSum enteric methane emissions per animal kg C animal 1 9 MethaneSum methan emissions by herbivorous per m2 kg C m 2 9 milk daily milk production kg m 2 d 1 7 milkanimal daily milk production per animal kg animal 1 d 1 7 milkanimalsum milk production per animal kg animal 1 7 milkc carbon in milk kg C m 2 d 1 9 milkcsum annual carbon in milk kg c m 2 9 milkn nitrogen in milk kg N m 2 d 1 7 milksum milk production kg m 2 7 MPyoung milk production of young cows kg animal 1 d 1 7 MPmature milk production of mature cows kg animal 1 d 1 7 MPwyoung potential milk production of young cows kg animal 1 d 1 7 MPwmature potential milk production of mature cows kg animal 1 d 1 7 MPposyoung possible milk production of dairy young cows kg animal 1 d 1 7 MPposmature possible milk production of dairy mature cows kg animal 1 d 1 7 n nitrogen substrate concentration in plant kg N kg 1 DM 7 n2denitrifsum annual dinitrogen los
49. ductivity NPP npp gpp rplant kg C m 2 7 nppd daily primary net productivity kg C m 2 d 1 7 nsym n concentration of symplast kg N m 2 7 Nsystem Nitrogen in the global system plant amp soil kg N m 2 7 ntot total substrate and structural nitrogen concentration per total plant dry matter kg N kg 1 7 ntransfer daily nitrogen from legume uptake kg N m 2 d 7 OMD Digestible organic matter 7 pa daily precipitations mm d 1 7 PAR PAR absorbed from leaves in canopy MJ m 2 7 pasum precipitations mm 7 Pc_1fwatpc factor controlling the effect of soil water content on photosynthesis and stomatal conductance 7 Pc_1pctl canopy leaf gross photosynthetic rate calculated at leaf temperature kg C m 2 d 1 9 Pc_ipmil canopy leaf gross photosynthetic rate calculated at air temperature Pcan g C m 2 d 1 7 phsoil soil ph 7 pmco2rep Light saturated leaf photosynthetic rate for reproductive stage micromol m 2 s 1 7 pmco2veg Light saturated leaf photosynthetic rate for vegetative stage micromol m 2 s 1 7 pmn factor controlling the effect of nitrogen on photosynthesis kg 2 m 2 d 1 7 70 psiroot root potential J kg 1 or kPa 7 raa aerodynamic resistance between canopy source height and reference height z s m 7 raboveplantS total plant respiration for shoot growth and maintenance at steady state kg C m 2 d 1 9 ractive microbial respiration for decomposition of C in active fraction of soil organic matter kg C m 2 d
50. e 3 The pasimvar file list of PaSim possible outputs 475 Ageing_1gamr20 Rate parameter for root turnover at 20 C d 1 7 Ageing_1gamsh20 Rate parameter for shoot turnover at 20 C d 1 7 age_ear1 age of biomass in the ear compartment d 7 age_ear2 age of biomass in the ear compartment d 7 age_ear3 age of biomass in the ear compartment d 7 age_ear4 age of biomass in the ear compartment d 7 age_lam1 age of biomass in the lam compartment d 7 age_lam2 age of biomass in the lam compartment d 7 age_lam3 age of biomass in the lam compartment d 7 age_lam4 age of biomass in the lam compartment d 7 age_stem1 age of biomass in the stem compartment d 7 age_stem2 age of biomass in the stem compartment d 7 age_stem3 age of biomass in the stem compartment d 7 age_stem4 age of biomass in the stem compartment d 7 apport_azote annual fertilization kg N m 2 7 BalCanimal animal carbon balance kg C m 2 7 BalCplant plant carbon balance kg C m 2 7 BalCsom soil carbon balance kg C m 2 7 BalCsystem carbon balance of the global system plants soil animals kg C m 2 7 BalCwc carbon substrate balance of plant kg C m 2 7 BalNanimal animal nitrogen balance kg N m 2 7 BalNmin nitrogen minimal balance of plant kg N m 2 7 BalNplant plant nitrogen balance kg N m 2 7 BalNsom soil nitrogen balance kg N m 2 7 BalNsystem nitrogen balance of the global system plants soil animals kg N m 2 7 BalNwn nitrogen substrate balance of plant kg N m 2 7
51. e root kg N m 2 7 Un_intotmax Maximum of total nitrogen concentation in plant kg N kg 1 DM 7 urinec carbon in urinate kg C m 2 d 1 9 urinecsum annual carbon in urinate kg C m 2 9 urinen nitrogen in urinate kg N m 2 d 7 urinensum annual nitrogen from hydrolysis of urine excreted by grazing animals kg N m 2 7 watersystem total water in the system mm 7 wc substrate carbon biomass of carbon substrate in plants kg C m 2 9 wcactive carbon in active fraction of soil organic matter kg C m 2 9 wemetabolic carbon in metabolic fraction of plant residue kg C m 2 9 wcorganic total organic carbon in soil kg C m 2 9 wcpassive carbon in passive fraction of soil organic matter kg C m 2 9 wcslow carbon in slow fraction of soil organic matter kg C m 2 9 westruct carbon in structural fraction of plant residue kg C m 2 9 westructlignin carbon in lignin of structural plant dry matter kg C m 2 9 wear ear component age 1 of shoot structural dry matter kg DM m 2 9 wear2 ear component age 2 of shoot structural dry matter kg DM m 2 9 wears ear component age 3 of shoot structural dry matter kg DM m 2 9 wear4 ear component age 4 of shoot structural dry matter kg DM m 2 9 Weightcalf Average weight of calves Kg 7 Weightcows Average weigth of cows Kg animal 1 7 Weightmature Average weight of mature cows Kg 7 Weightyoung Average weight of young cows Kg 7 wg plant structural dry matter kg struct DM m 2 7 wgn nitrogen in structural
52. ecosystems functioning such as heat and water balance effects on the vegetation and heat stress effects on livestock production It has been already involved in long term simulations to assess climate change impacts PaSim is therefore a useful research tool to study climate change impacts on livestock systems and to investigate adaptation options 1 7 Work in progress PaSim is currently developed to e Vegetation Simulate a legume dynamics and the dynamics of community scale plant functional traits in response to climate and to agricultural practices e Management Improve the two step procedure which allows determining the optimal stocking rate and fractional coverage of grazing at the forage system scale so that it can account for past climate instead of future climate and for the role of conserved forage in ensuring the security of the feeding systems by disposing of sufficient reserves to meet production hazards e Climate Simulate tropical grasslands in the framework of the ANR Projet EPAD 2010 2013 http epad cirad fr 10 Hourly Data VARIABLE DESCRIPTION UNIT Pa Precipitations mm d Ta Average air temperature K U Wind speed m s IATMtot Radiation W m Ea Water vapour pressure kPa CO2 CO atmospheric ppm concentration NH3 NH3 atmospheric ppm concentration Daily Data VARIABLE DESCRIPTION UNIT Tamax Daily max air temperature C Tamin Daily min air temperature C Pa Daily
53. f animal 1 dairy cows 2 suckler cows 3 01d module for dairy cows c 125 Calving date for dairy or suckler livestock systems d 280 Suckling period for suckler livestock systems Cd 280 Age of the calves exit for suckler livestock systems d 0 19 Proportion of young suckler cows 3 or 4 years old or primipare dairy cov 60 25 calf birth weight for suckler livestock systems kg 10 10 Maximum theoretical milk production kg animal d 0 125 Quantity of concentrate provided per kg of milk kg DM kg of milk 1 09 Concentrate ener dy value CUF kg 0 91 Forage energy value CUF kg 0 96 Forage fill value CUE kg 0 120 N fraction in the forage kg N kg 0 120 N fraction in the concentrate kg N K9 625 0 650 0 Live weight of cows for autogestion first young second Mature 225 2425 Body score condition of cows for autogestion first young second Mature 32 0 44 0 Age of cows for autogestion first young second Mature in months Figure 4 Example of an initial conditions file 18 19 2 1 2 Names input file This file figure 5 contains the path and the name of management initial and site specific conditions as well as weather data file This information must respect the following order e Site specific conditions file Initial conditions file Management file Air temperature data file Water vapour pressure data file Wind speed data file Global radiation data file Precipitation data file NH data file CO data file TextPad
54. g C m kg N m kg N m kg N m kg m kg m kg m kg m kg m kg m kg m kg m kg m kg m kg m 74 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 wst 4 llam 1 llam 2 llam 3 llam 4 Ist 1 Ist 2 Ist 3 Ist 4 tsoil 1 tsoil 2 tsoil 3 tsoil 4 tsoil 5 tsoil 6 ssw snow thetas 1 thetas 2 thetas 3 thetas 4 thetas 5 thetas 6 nfertammundissolved nfertnitundissolved nno2 1 nno2 2 nno2 3 nno2 4 nno2 5 nno2 6 nn2odenit 1 nn2odenit 2 nn2odenit 3 nn2odenit 4 nn2odenit 5 nn2odenit 6 snowfallsum lessum lecsum freezingsum snowmeltsum rainsum snowfallsumprev lessumprev freezingsumprev snowmeltsumprev rainsumprev wr wr2 wr3 wr4 stem shoot structural dry matter in fourth age component lamina leaf area index in first age component lamina leaf area index in second age component lamina leaf area index in third age component lamina leaf area index in fourth age component stem leaf area index in first age component stem leaf area index in second age component stem leaf area index in third age component stem leaf area index in fourth age component Temperature in soil layer 1 Temperature in soil layer 2 Temperature in soil layer 3 Temperature in soil layer 4 Temperature in soil layer 5 Temperature in s
55. ginning of the considered grazing period AGE_cow_M Month Age for primiparous cows at the start of the considered grazing period Forage quantity kg DM animal Age for multiparous cows at the start of the day considered grazing period Table 10 the animal tab parameters 47 3 6 The animal tab PaSim Laqueuille_int File Run Results Mode Overview Plant Soil Meteo Cut amp Fert OutPuts Properties Mame Potential eating rate of lactating cows kg animal Weight of lactating cows kg Type of animal 1 Dairy 2 Suckler 3 Old Module 4 Dairy heifers 5 Suckler heifers 6 sheep Calving date for dairy or suckler livestock system d Suckling period for suckler livestock system d Age of the calves exit for suckler livestock systems d Proportion of young suckler cows 3 or 4 years old or primipare dairy cows in the cattle Calf birth Weight for suckler livestock systems kg Max potential milk production Kg cow d First A Zu rare 5 0 Nanimal Tanimal Danimal LWYcows LWMcaws BCSYcows BCSMc LWealves AGE co AGE co Forage 15 33333E 4 141 14 0 405 0 0 0 0 0 0 0 0 0 0 0 H 0 0 3 5E 4 jiss jmo 418 0 0 0 no lo 0 12 83333E 4 169 31 0 0 0 0 0 F 0 0 H 0 0 DE 4 i 13 83333E 4 Nanimal Tanimal Danimal LWY cows BCSYcows bic AGE_co AGE_co 2 13523E 4 129 6 0 454 0 N 0
56. hest position of the sun Slope rad Aspect rad Height above sea level Micrometric reference height above soil surface NH reference height above soil surface Number of soil layers Cumulated depth of soil layers Cumulated depth of lower soil boundary layer mm Maximal canopy height Canopy height parameter leaf area index for which canopy is half the maximum cannopy height Clover fraction Relative root dry matter in different soil layers Soil depth below which there is neither plant N uptake nor soil texture effect of active SOM decomposition Bulk density of each soil layer Sand fraction of texture Clay fraction of texture Silt fraction of texture Saturated soil water content Saturated soil water content of lower boundary layer Air entry potential Air entry potential of lower soil boundary layer Parameter b in psi Parameter b of lower soil boundary layer Saturated hydraulic conductivity Saturated hydraulic conductivity of lower soil boundary layer Parameter for the determination of the field capacity Field capacity Permanent wilting point Soil pH Parameter a for Freundlich equation for soil NH4 partitioning Parameter b for Freundlich equation for soil NH4 partitioning a s l above sea level calculated by of the soil routine of Pierluigi Calanca UNIT rad h min rad rad ma s l m a s l m a s l mm mm m m laminae m kg kg fraction mm d 1 mm d 1 HELP
57. ht of young primiparous cows at the beginning of the considered grazing period Initial average live weight of mature multiparous cows at the beginning of the considered grazing period Initial average body condition score of young primiparous cows at the beginning of the considered grazing period Initial average body condition score of mature multiparous cows at the beginning of the considered grazing period Initial average liveweight of calves at the beginning of the considered grazing period Age for primiparous cows at the start of the considered grazing period Age for multiparous cows at the start of the considered grazing period Forage quantity supply to supplement cows at pasture UNIT Julian day Julian day kg N m 2 kg N m 2 animal m Julian day day kg N m 2 kg N m 2 kg N m 2 kg animal kg animal kg animal Month Month kg DM animal d Table 2 Description of management variables needed in PaSim input Soil input exemple txt z fclay fsilt fsand rhob Osat m kg m 3 m3 m 3 0 02 0 54 0 32 0 13 591 0 53 0 05 0 54 0 32 0 13 591 0 53 0 1 0 54 0 32 0 13 742 0 53 0 3 0 56 0 32 0 12 874 0 46 0 51 0 57 0 33 0 1 1205 0 46 OS na RE 1205 0 46 Input site name max 100 letters exemple Input number of soil layers max 10 6 3 Test layers exemple txt 020 050 100 300 510 700 z Psie b ksat Qsat 0 000 m mm mm d m3 m3 nn 0 020 589 126 13 908 24 995 0 530 dun
58. iated stocking rate at the forage system scale First PaSim simulates a cut meadow and optimizes cutting events and mineral N fertilization to determine the optimal forage yield In this way it estimates the available forage resources Y to feed animals at barn Second the model simulates a grazed pasture and according to Y it increments the instantaneous stocking rate S until an equilibrium between forage resources Y and forage needs X is reached while accounting for available surfaces for either mowing 1 F or grazing F Figure 7 X is calculated as the product of the number of days animals spend at barn Ng by the average intake capacity C of animals at barn assumed to be 15 5 kg DM animal d and S The procedure stops when with a tolerated error of 1 Yd F X N CIS 26 27 Using F and S values the procedure allows calculating the stocking rate D per ha of total grassland surfaces D FS 8 At barn DMI y lt Knrake roterance VDMI y Si SS SH 7 DMI 32 Kiniake roterance VDMI Forage requirements Forage ressource kg DM ha of grazed land kg DM ha of grazed land Va 2 Stocking rate optimization 1 Cutting and inorganic N fertilization Balance Grazing days 1 F Optimal Nu Fraction of grazed land S S 0 1 Optimal Sa 02 gt SP D stocking rate Instantaneous stocking rate Stocking rate at farm scale
59. inininincnnonos 36 3 Graphical User Interface ss 38 3 1 The overview IQ ns cu one mue 38 32 TODA A ain 40 83 TMesSdltabDi Se en en en 42 3 4 The meteo ab cosi dla 44 3 5 The Cut and Fert tab aaa A 46 36 The NINA NH cc heehee nr 48 3 7 The outputs tab nenne een 50 3 8 The properties Tab ea inanste 52 3 9 The sensibility analyse tab i 54 3 10 The expettimode ail 56 4 F IRTONCOS een nenne 58 Annexe 1 Usual Tree Structure of PaSim 60 Annexe 2 Example of management file 61 Annexe 3 The pasimvar file list of PaSim possible outputs 66 Annexe 4 restart file of PaSim restart txt version without 4C 74 Annexe 5 restart file of PaSim restart txt fC version 77 INPUT OUTPUT C limate Radiation Precipitation Temperature Vapor pressure Wind speed Soil Vegetation Texture Multi or SWC monospecies Conductivity With or without Density legumes Depth Herbivores Management Type heifers Mowing suckler or dairy N fertilization cows sheeps Grazing LW BCS age Tillage MP at pot max turnout to grass Fluxes States GHG CO N O CH Forage provision C N H O amp energy MP LW and BCS fluxes SOM SWC Optimized management Mowing gt N fertilization Grazing gt Irrigation Figure 1 Description of the
60. ion of initial conditions variables needed in PaSim input ADVISED VALUE 0 04 0 002 0 022 0 001 0 814 0 052 0 001 0 001 0 001 0 001 0 001 0 001 0 00025 0 00035 283 8 3 6 0 00000145 0 00000151 0 15 650 0 20 45 8 10 for suckling systems 28 34 for dairy systems 0 125 0 120 0 120 600 650 33 32 44 17 2 1 1 4 Initial conditions file Initial condition file Tab 4 and Figure 4 describes initial conditions for plant soil and grazing animals It contains also information about vegetation management An example of this file is given below NB Initial soil organic matter SOM pool values could be either given by PaSim user if known but it is rarely the case and when total SOM is known it is difficult to share it between the 10 SOM pools of PASIM or obtained by running the model to reach SOM equilibrium See 6 3 for more explanations P oens init_cond Bloc notes Fichier Edition Format Affichage 9 15 Initial condition of shoot dry matter kg m 2 EEE EDI le OAL ONE OSE DER ORES OL Db Kc shoot dry matter after cutting Ckag m 25 0 58 Initial condition of root dry matter Ckg m 2 1 Initial condition of LAI m 2 m 2 0 4 0 4 0 4 0 4 0 4 0 4 0 4 0 4 0 4 0 4 LAI after cutting 0 04 Initial cond for plant C substrate concentration kg C kg 0 002 Initial cond for plant N substrate concentration kg N kg 0 022 Initial cond for N conc of struct plane dry matter kg N kg 0 814 I
61. ity RH use Bolton 1980 Ea 0 6112 exp 17 67 Ta Ta 243 5 RH 100 Where Ta is in C 380 could be set as default value 2 could be set as default value Table 8 the meteo tab parameters 43 3 4 The meteo tab PaSim Laqueuille_int File Rum Results Mode Overview Plant Soil Cut amp Fert Animal OutPuts Properties CO2 atmospheric concentration ppm NH3 atmospheric concentration ppm 380 0 20 Load all meteo files Valid Reset Ann e Pa mm d 1 Tamin K Tamax K Tamoy k U m s 1 TATM W m 2 EA kPa 1 1105 75 0 0 564 0 3 0298 3 0295 3 0295 3 0295 2 1012 5 0 0 816 0 2 774 2 774 2 774 2 774 3 987 5 0 0 588 0 2 705 2 7055 2 7055 2 7055 4 821 0379 0 0 372 0 12 2908 12 2494 2 2494 2 2494 5 1118 3 0 0 364 8 15 0638 3 0638 3 0638 13 0638 6 1362 0 0 0 paz 3 7315 3 7318 3 7315 3 7315 7 1129 0 10 0 355 2 Su 3 0932 3 0932 3 0932 8 1043 5 0 0 456 0 2 8589 2 8589 2 8589 2 8589 Figure 11 Meteo tab of the graphical interface HE In this tab the user has to load the meteo files associated to the grassland These files are in the Meteo directory of the grassland Only the CO and the NH3 parameters can be changed They are considered to be constant during the simulation If not then manually change links to CO or NH files into the names_inputs_file before running PaSim If the user u
62. kt thermal conductivity of soil layers w m 2 k 2 kturnrt root turnover rate including water and LAI limitations d 1 7 kturnsh shoot turnover rate including water and LAI limitations d 1 7 lai leaf area index LAI m2 leaf m 2 soil 7 le latent heat flux w m 2 7 leach daily nitrate leaching vertical tansfert between soil layers kg N m 2 d 1 2 leach_1 daily nitrate leaching in the soil layer 1 kg N m 2 d 1 7 leach_2 daily nitrate leaching in the soil layer 2 kg N m 2 d 1 7 leach_3 daily nitrate leaching in the soil layer 3 kg N m 2 d 1 7 leach_4 daily nitrate leaching in the soil layer 4 kg N m 2 d 1 7 leach_5 daily nitrate leaching in the soil layer 5 kg N m 2 d 1 7 leach_6 daily nitrate leaching in the soil layer 6 kg N m 2 d 1 7 leach_nsoil daily nitrate leaching in the last the deepest soil layer kg N m 2 d 1 7 leachn2o nitrous oxide leaching kg N m 2 d 1 2 leachsum nitrate leaching kg N m 2 7 lecsstep extraction of water by the root integrated on a step of time mm step of time 2 lecs extraction of water by the root for all soil layers mm 2 lesstep soil evaporation integrated on a step of time mm step of time 7 llam1 lamina component age 1 of leaf area index m2 m 2 7 llam2 lamina component age 2 of leaf area index m2 m 2 7 llam3 lamina component age 3 of leaf area index m2 m 2 7 llam4 lamina component age 4 of leaf area index m2 m 2 7 loss dry matter lost by cuts kg DM m 2 7 lossc carbon in
63. ll input files Section 2 1 1 The pasimvar file updated according to paSim executable The PaSim run file Section 2 1 3 ex site pasim The file containing the list of input file path The executable pasim exe Then PaSim can be launched by using the following command pasim exe site pasim 2 2 2 Multi year simulations As compared to a standard single year simulation the setup of a multi year simulation requires only two additional steps e Setting the parameter TSTOP at the total number of days to be simulated e g TSTOP 3650 1 to ensure PaSim will write the last year for a 10 years simulation NB PaSim does not simulate bissextile years e Setting the parameter CYCLE METEO at the number of years simulated e g CYCLE_METEO 10 in the previous example 22 B Second part SOMERRORMAX RESTART_FILE_IN RESTART_FILE_OUT PARAM_SLAM PARAM_TREP PARAM_FCLOVER PARAM_ZETA PARAM_SSTA PARAM_KCN PARAM_FNREF PARAM_CWPL PARAM_HCANHALF PARAM_UNSIGMA20 PARAM_FREQ_PLOUGHING PARAM_TASUMREP PARAM_TBASE PARAM_NDFEAR PARAM_NDFLAM PARAM_NDFSTEM PARAM_HCANMAX PARAM_NTOTMAX PARAM_KTURNRT20 PARAM_KTURNSH20 PARAM_FCSH PARAM_FCR PARAM_DAH PARAM_DEVEAR FLAG_ROOT_PROFILE B_ROOT_PROFILE PARAM_FROOT PARAM_PMCO2VEG PARAM_PMCO2REP PARAM_A_NH4 PARAM_B_NH4 PARAM_YIELDLOSS PARAM_DNDFLAMI1 4 PARAM_DNDFSTEM 1 4 PARAM_DNDFEAR 1 4 NB_FICHIERS_ PAR NB_POINTS_TERRE NB_POINT_METEO NUM_POINT_TRAV
64. lso a reset button which put all the parameters to their default value 3 1 The overview tab PaSim Laqueuille_int File Run Results Mode Overview Plant Soil Meteo Cut amp Fert Animal OutPuts Properties Deg Min Sec Height above sea level m a s l 1040 0 Micrometic ref height soil m a s l ao Slope rad 00 NH3 Reference height soil m a s l po Aspect rad 00 NH4 Deposition kg M m 2 d 1 1 4566 Zenith time h min 1212 NO3 Deposition kg N m 2 d 1 1 516 Figure 8 Overview tab of the graphical interface In this tab the user can fill specifics values of the grassland such as the latitude or the zenith time 38 ADVISED VARIABLE UNIT HELP VALUE Description Latitude N exemple 55 52 20 rad 11 2 11 2 Exemple 55 52 60 20 3600 2 17 360 Height above sea level m a s l Slope rad Tr Tr or 0 2 Tr 0 0 Aspect rad Tr tr or 0 2 Tr 0 0 Zenith time h min 0 24 12 12 Micrometric reference height above soil surface m a s l 2 0 NH reference height above soil surface m a s l 2 0 NH deposition other than gaseous NH3 kg N m2d Prefer default value 0 00000145 NO3 deposition kg N m2d Prefer default value 0 00000151 Table 5 the overview tab parameters ADVISED VARIABLE UNIT HELP VALUE Maximal canopy height m Canopy height parameter leaf area index for m laminae m Doe
65. m3 m3 Saturated soil water content of lower soil boundary layer m3 m3 Air entry potential mm Air entry potential of lower soil boundary layer mm Parameter b in psi Parameter b of lower soil boundary layer Saturated hydraulic conductivity mm d Saturated hydraulic conductivity of lower soil boundary layer mm d Parameter for the determination of the field capacity Field capacity Permanent wilting point Soil pH Parameter a for soil NH4 partitioning Figure 3 Example of a site specific conditions file 16 VARIABLE Initial condition of shoot dry matter Shoot dry matter after cutting Initial condition of root dry matter Initial condition of LAI LAI after cutting Initial cond for plant C substrate concentration Initial cond for plant N substrate concentration Initial cond for N conc of structural plant dry matter Initial cond for C in structural dead plant material Initial cond for C in metabolic dead plant material Initial cond for C in active soil organic matter Initial cond for C in slow soil organic matter Initial cond for C in passive soil organic matter Initial cond for N in metabolic dead plant material Initial cond for N in active soil organic matter Initial cond for N in slow soil organic matter Initial cond for N in passive soil organic matter Initial cond for soil ammonium Initial cond soil nitrate Initial condition for soil water content Capillary rise from lower boundary laye
66. mal processes at barn the latter are estimated ii Neither mixed management cutting and grazing in a given paddock nor between year forage stock use is considered iii Livestock systems are assumed self sufficient in terms of feed supply during housing animals are fed with hay derived from the cut herbage 28 29 2 3 2 How to run the procedure for optimal grazing coverage and stocking rate In the following example optimal grazing coverage and stocking rate of site1 are optimized on two successive meteorological years for instance year1 and year2 For running the first step automatic cutting and N fertilization on year1 1 you have to create e 1 PaSim specific run file e g sitel_year1_cut pasim e 1 specific management file e g site1_year1 management_cut dat e 1 specific file for input data file paths e g names_files input_sitel_year1_cut txt The management file for automatic cutting e g site _year1 management_cut dat must have the following information still 180 columns tcut 500 500 500 500 500 500 500 500 500 500 tfert 500 500 500 500 500 500 500 500 500 500 Nfertamm 0000000000 Nfertnit 0000000000 Nanimal 0000000000 tanimal 500 500 500 500 500 500 500 500 500 500 danimal 0000000000 Nligmanure 0000000000 Nslurry 0000000000 Nsolmanure 0000000000 LWYcows 0000000000 LWMcows 0000000000 BCSYcows 0000000000 BCSMcows 0000000000 LWcalves 0000000000 AGE_cow_P 0000000000 AGE_cow_M 0000000000
67. metabolic dead plant material kg N m Initial cond for N in active soil organic matter kg Nm Initial cond for N in slow soil organic matter kg Nim Initial cond For N in passive soil organic matter kg N m Initial cond for soil ammonium kg Nm Initial cond soil nitrate kg N m Qu n an Figure 17 Soil tab of the graphical interface in expert mode The number of soil layer can t be changed 56 PaSim Laqueuille_int File Run Results AGE RESTART_FILE_OUT NONE or C B_ROOT_PROFILE C PARAM_FCLOVER PARAM_FROOT PARAM_SLAM PARAM_TREP PARAM_TASUMREP PARAM_TBASE PARAM_NDFEAR PARAM_NDFLAM PARAM_NDFSTEM PARAM_HCANMAX PARAM_NTOTMAX PARAM_KTURNRTZO PARAM_KTURNSH20 PARAM_FCSH PARAM_FCR PARAM_DAH PARAM_DEVEAR PARAM_PMCO2VEG PARAM_PMCO2REP O PARAM_ZETA CI PARAM_SSTA C PARAM_KCN PARAM_FNREF O PARAM_CWPL CO PARAM_UNSIGMAZO DD PARAM_HCANHALF Figure 18 Properties tab of the graphical interface in expert mode 0 noose the 3 4 5 6 0 248 0 164 0 041 0 0040 0 05 0 018 0 005 ch to SOWN mode PARAM_DNDFEAR 1 PARAM_DNDFEARZ PARAM_DNDFEARS PARAM_DNDFEAR4 PARAM_DNDFSTEMI PARAM_DNDFSTEM2 PARAM_DNDFSTEM3 PARAM_DNDFSTEM4 PARAM_DNDFLAMI PARAM_DNDFLAM2 PARAM_DNDFLAMS PARAM_DNDFLAM4 NB_FICHIERS_PAR NB_POINTS_TERRE NB_POINT_METEO NB_MANAGEMENT NUM_POINT
68. mmonium fertilization with previous year fertilization kg N m 2 7 nfertammtotyear annual total N ammonium fertilization without previous year fertilization kg N m 2 7 nfertnittot total N nitrate fertilization with previous year fertilization kg N m 2 7 nfertnittotyear annual total N nitrate fertilization without previous year fertilization kg N m 2 7 Nfert Daily N fertilization optimized by the model according to INN kg N m 2 d 1 7 NfertSum Cumulated N fertilization optimized by the model according to INN kg N m 2 7 nn20 n2o content in soil layer h kg N m 2 2 nn2odenit nitrous oxide content in the denitrification pool kg N m 2 2 nn2ogas_1 N20 gaz into the soil layer 1 7 nn2ogas_ 2 N20 gaz into the soil layer 2 7 nn2ogas_3 N20 gaz into the soil layer 3 7 nn2ogas_4 N20 gaz into the soil layer 4 7 nn2ogas_5 N20 gaz into the soil layer 5 7 nn2ogas_6 N20 gaz into the soil layer 6 7 nnit nitrate n in soil layer h kg N m 2 2 nnit_1 N nitrate in first soil layer kg N m 2 7 nnit_2 N nitrate in second soil layer kg N m 2 7 nnit_3 N nitrate in third soil layer kg N m 2 7 nnit_4 N nitrate in fourth soil layer kg N m 2 7 nnit_5 N nitrate in fifth soil layer kg N m 2 7 nnit_6 N nitrate in sixth soil layer kgN m 2 7 nnittot total nitrate n in soil kg N m 2 7 nno2 NO2 content in soil layer h kgN m 2 2 Nplant total substrate structural and cuticule plant nitrogen kg N m 2 7 npp net primary pro
69. nitial cond for C in struct dead plant material kg C m 2 0 052 Initial cond for c in metabolic dead plant material dg C m 2 0 001 Initial cond for C in active soil organic matter kg C m 2 0 001 Initial cond for C in slow soil organic matter kg C m 2 0 001 Initial cond for C in passive soil organic matter kg C m 2 0 0043 Initial cond for N in metabolic dead plant material deg N m 2 0 001 Initial cond for N in acive soil organic matter kg N m 2 0 001 Initial cond for N in slow soil organic matter kg N m 2 0 001 Initial cond for N in passiv soil organic matter tig nN m 2 0 0004 Initial cond for soi ammonium kg N m 2 0 0004 Initial cond for soil nitrate kg N m 2 0 35 0 35 0 35 0 35 0 35 0 35 Initial condition for soil water content m 3 m 3 0 0 capillary rise from lower boundary layer yes 1 0 or no 0 0 0 43 water content of lower soil boundary layer in spring m 3 m 3 0 38 water content of lower soil boundary layer in autumn m 3 m 3 283 29 Average temperature of lower soil boundary layer CK 7 6 Amplitude of temperature of lower soil boundary layer Ck 3 89 Phase of temperature of lower soil boundary layer Crad 0 00000145 NH4 Deposition other than gaseous NH3 kg N m 2 d 1 0 00000151 NO3 Deposition kg N m 2 d 1 0 Dates of cutting and grazing calc by model 1 or on input 0 9 0 Potential eating rate for lactating cows C kg GvE m 2 400 0 weight of lactating cows kg 3 Type o
70. number of characters N PaSim westructlignin Westructlignin_CO2 nn2o 1 nn20 2 nn2o 3 nn2o 4 nn2o 5 nn2o 6 namm 1 namm 2 namm 3 namm 4 namm 5 namm 6 nnit 1 nnit 2 nnit 3 nnit 4 nnit 5 nnit 6 nammsurface wcactive wcactive_CO2 wnactive wcstruct wcstruct CO2 ncuticle wcmetabolic wemetabolic_CO2 wnmetabolic wcslow weslow_C02 wnslow wcpassive wcpassive_CO2 wnpassive wc wc_C14 wnapo wnsym wgn wlam 1 Variables Carbon in the lignin of the structural dead dry matter C14 or C13 fraction in carbon in the lignin of the structural dead dry matter N20 in soil layer 1 N20 in soil layer 2 N20 in soil layer 3 N20 in soil layer 4 N20 in soil layer 5 N20 in soil layer 6 Ammonium in soil layer 1 Ammonium in soil layer 2 Ammonium in soil layer 3 Ammonium in soil layer 4 Ammonium in soil layer 5 Ammonium in soil layer 6 Nitrate in soil layer 1 Nitrate in soil layer 2 Nitrate in soil layer 3 Nitrate in soil layer 4 Nitrate in soil layer 5 Nitrate in soil layer 6 ammonium in soil surface layer Carbon in active fraction of plant residue C14 or C13 fraction in carbon in active fraction of plant residue Nitrogen in active fraction of plant residue Carbon in structural fraction of plant residue C14 or C13 fraction in carbon in structural fraction of plant residue Nitrogen in leaf cuticle Carbon in metabolic fraction of plant residue C14 or C13 fraction in Carbon in metab
71. of for automatic management kg Only used for automatic management 600 for young or primarous Initial cow liveweight of for automatic management kg Only used for automatic management 650 for mature or multiparous Initial cow body condition score for automatic Only used for automatic management 3 management for young or primarous Initial cow body condition score for automatic Only used for automatic management 3 management for mature or multiparous Initial cow age for automatic management for months Only used for automatic management 32 young or primarous Initial cow age for automatic management for months Only used for automatic management 44 mature or multiparous Nanimal Animal m stocking rate Tanimal Julian day start of the grazing period Danimal day Length of the grazing period LWYcows kg animal Initial average live weight of young cows at the beginning of the considered grazing period LWMcows kg animal Initial average liveweight of young primiparous cows at the beginning of the considered grazing period BCSYcows Initial average live weight of mature multiparous cows at the beginning of the considered grazing period BCSMcows Initial average body condition score of young primiparous cows at the beginning of the considered grazing period LWcalves kg animal Initial average body condition score of mature multiparous cows at the beginning of the considered grazing period AGE_cow_P Month Initial average liveweight of calves at the be
72. oil layer 6 Soil surface liquid water Snow cover Volumetric water content in soil layer 1 Volumetric water content in soil layer 2 Volumetric water content in soil layer 3 Volumetric water content in soil layer 4 Volumetric water content in soil layer 5 Volumetric water content in soil layer 6 Ammonium from mineral fertilisation undissolved Nitrate from mineral fertilisation undissolved NO in soil layer 1 NO in soil layer 2 NO in soil layer 3 NO in soil layer 4 NO in soil layer 5 NO in soil layer 6 N20 content in the denitrification pool of soil layer 1 N20 content in the denitrification pool of soil layer 2 N20 content in the denitrification pool of soil layer 3 N O content in the denitrification pool of soil layer 4 N O content in the denitrification pool of soil layer 5 N O content in the denitrification pool of soil layer 6 Yearly sum of snow fall Sum of soil evaporation Sum of plant transpiration Frozen water Slush Yearly sum of rain fall Does not contain anything anymore Yearly sum of snow fall from previous time step Sum of soil evaporation from previous time step Frozen water at previous time step Slush at previous time Yearly sum of rain fall at previous time step Does not contain anything anymore root structural dry matter of age 1 root structural dry matter of age 2 root structural dry matter of age 3 root structural dry matter of age 4 19 100 regcount counter for number of
73. olic fraction of plant residue Nitrogen in metabolic fraction of plant residue Carbon in slow fraction of plant residue C14 or C13 fraction in Carbon in slow fraction of plant residue Nitrogen in slow fraction of plant residue Carbon in passive fraction of plant residue C14 or C13 fraction in Carbon in passive fraction of plant residue Nitrogen in passive fraction of plant residue Carbon substrate in plant C14 or C13 fraction in Carbon substrate in plant biomass of nitrogen substrate in apoplast biomass of nitrogen substrate in symplast Nitrogen in structural dry matter lamina shoot structural dry matter in first age component Unit s kg C m Ba kg kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg N m kg C m Bq kg kg N m kg C m Bq kg kg N m kg N m Bq kg kg C m kg C m Ba kg kg N m kg C m Bq kg kg N m kg C m Ba kg kg N m kg N m kg N m kg m 77 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 wlam 1_C14 wlam 2 wlam 2_C14 wlam 3 wlam 3_C14 wlam 4 wlam 4_C14 wear 1 wear 1_C14 wear 2 wear 2_C14 wear 3 wear 3_C14 wear 4 wear 4_014 wst 1 wst 1_C14 wst 2 wst2_C14 wst 3 wst 3_C14 wst 4
74. ot for the layer 5 mm 166 lecs 6 Water extracted by the root for the layer 6 mm 167 Storage_rC Carbon labile conentration in plant kg C m2 168 Storage rC_C14 C14 or C13 fraction in Carbon labile conentration in plant Ba kg 169 Storage_rrC Carbon stable conentration in plant kg C m2 170 Storage_rrC_C14 C14 or C13 fraction in Carbon stable conentration in plant Bq kg 171 Storage_rN Nitrogen labile conentration in plant kg N m2 172 Storage _rrN Nitrogen stable conentration in plant kg N m2 80
75. over daily variation of the legume fraction d 1 7 diffn20_1 diffn2o l interface de la premi re couche 7 diffn20_2 diffn2o l interface de la seconde couche 7 diffn20_ 3 diffn2o l interface de la troisi me couche 7 diffn20_4 diffn2o a l interface de la quatrieme couche 7 diffn20 5 diffn20 l interface de la 5 me couche 7 diffn20_6 diffn2o l interface de la 6 me couche 7 66 diffn2odenit_1 diffn2odenit l interface de la premiere couche 7 diffn2odenit_2 diffn2odenit a l interface de la seconde couche 7 diffn2odenit_3 diffn2odenit a l interface de la troisi me couche 7 diffn2odenit_4 diffn2odenit l interface de la quatri me couche 7 diffn2odenit 5 diffn2odenit l interface de la 5 me couche 7 diffn2odenit 6 diffn2odenit l interface de la 6 me couche 7 DMicalf Dry matter ingested by calves Kg animal 1 7 DMimature Dry matter ingested by mature suckler cows Kg animal 1 7 DMlyoung Dry matter ingested by young suckler cows Kg animal 1 7 DMIcyoung Concentrate ingested by young dairy cows Kg animal 1 7 DMicmature Concentrate ingested by mature dairy cows Kg animal 1 7 DMifyoung Forage ingested by young suckler cows Kg animal 1 7 DMlfmature Forage ingested by mature suckler cows Kg animal 1 7 dn2o variation of nitrous oxide soil pool kg N m 2 d 1 2 dn20_1 d riv e de nn2o l interface de la premi re couche 7 dn20_2 d riv e de nn2o
76. pasim file of the grassland cf PASIM run file page 22 The user can also generate the pasim file associate to this tab 52 53 3 9 The sensibility analyse tab PaSim Laqueuille_int File Run Results MUGEN Overview Plant s Expert Mode CHI E Outputs Properties Sensibility Analyse Sensibility analyse Variables Values variables Values Min Max o Nb of values Function f F Restart File All with the same file v gt gt Generate Files lt lt Figure 16 Sensibility tab of the graphical interface This tab appears only if the user wants to and allows to generate all the needed files to perform a sensitivity analyse 54 Number of soil layers Parameter a for Freundlich equation for soil NH4 partitioning Parameter b for Freundlich equation for soil NH4 partitioning Initial cond for C in structural dead plant material Initial cond for C in metabolic dead plant material Initial cond for C in active soil organic matter Initial cond for C in slow soil organic matter Initial cond for C in passive soil organic matter Initial cond for N in metabolic dead plant material Initial cond for N in active soil organic matter Initial cond for N in slow soil organic matter Initial cond for N in passive soil organic matter Initial cond for soil ammonium Initial cond soil nitrate Initial condition for soil water content
77. profile iii soil organic matter pools are usually initialized to values closed to their steady state equilibrium values after a spin up run PaSim still fails to faithfully reproduce timing duration and magnitude of peak emissions triggered by the application of mineral and organic fertilizers and by rain events Calanca et al 2007 z aiming at understanding the C and N cycles carbon sequestration greenhouse gases emissions GHG and the effects of climate variability and climate change on grasslands 8 e Cattle PaSim representation of cattle does not consider i differences in individual energy needs and reproduction cycle ii diet chemical composition and animal breed for enteric CH4 iii the herbage digestibility dependance of factors used to convert metabolizable energy intake into CH4 production conversion factors are assumed constants for suckler cows and heifers e Environment The simulation of grassland ecosystems does not allow simulating i the possible effects of diseases pests and weeds on grassland production ii tropical soil climate conditions 1 6 Model strengths PaSim simulates thoroughly and mechanistically i Energy C N and water balance of grassland ecosystems ii Forage provisioning iii Performance of grazing ruminants iv Potential to sequester C in grassland soils v GHG emissions at pasture including ecosystem respiration N2O and enteric CH vi Climatic effects on grassland
78. r yes 1 0 or no 0 0 Water content of lower soil boundary layer in spring Water content of lower soil boundary layer in autumn Average temperature of lower soil boundary layer Amplitude of temperature of lower soil boundary layer Phase of temperature of lower soil boundary layer NH deposition other than gaseous NH3 NO deposition Dates of cutting and grazing calc by model 1 or on input 0 Potential eating rate of lactating cows Weight of lactating cows Type of animal Calving date for dairy or suckler livestock system Suckling period for suckler livestock system Age of the calves exit for suckler livestock systems Proportion of young suckler cows 3 or 4 years old or primiparous dairy cows in the cattle Calf birth Weight for suckler livestock systems Milk production at peak Quantity of concentrate provided per kg of milk Concentrate energy value Forage energy value Forage fill value N fraction in the forage N fraction in the concentrate Initial cow liveweight of for automatic management Initial cow body condition score for automatic management Initial cow age for automatic management first young primiparous second mature multiparous UNIT kg DM m kg DM m kg DM m m laminae m m laminae m kg C kg DM kg N kg DM kg N kg DM kg C m kg C m kg Cm kg C m kg C m kg N m kg N m kg N m kg Nm kg Nm kg Nm mem D D D D D HHH D D N Rad kg Nm d kg
79. regrowths 101 devstage Development stage 102 tameani Average air temperature 6 days before K 103 tamean2 Average air temperature 5 days before K 104 tamean3 Average air temperature 4 days before K 105 tamean4 Average air temperature 3 days before K 106 tamean5 Average air temperature 2 days before K 107 tamean6 Average air temperature 1 day before K 108 tameand Average air temperature K 109 tacumm Sum of daily average temperature K 110 tacummprev Sum of daily average temperature for previous day K 111 tasumd Sum of efficient temperature K day 112 tcutO Julian day for first cut day 113 tayearsum Yearly air sum temperature K 114 hsteadystate Number of meteo cycle when searching for equilibrium 115 nanimaltot Stocking rate animal m 116 nfertammtot Total ammonium fertilisation with previous year Kg N m 117 nfertnittot Total nitrate fertilisation with previous year Kg N m 118 fertcount Counter for fertilisation application 119 gmean 1 Average growth rate during regrowth for plant layer 1 kg m d 120 gmean2 Average growth rate during regrowth for plant layer 2 kg m d 121 gmean 3 Average growth rate during regrowth for plant layer 3 kg m d 122 gmean 4 Average growth rate during regrowth for plant layer 4 kg m d 123 gmean 5 Average growth rate during regrowth for plant layer 5 kg m d 124 gmean 6 Average growth rate during regrowth for plant layer 6 kg m d 125 gmean 7 Average growth rate during regrowth for plant layer 7 kg m d 1
80. s PaSim searches for equilibrium between forage ressources and cattle forage needs at barn by iterative runs At the end of the simulation PaSim creates a new file which contains in that order i Proportion of forage requirements relatively to the forage available ii Fractional grazing coverage ii Number of days spent at pasture d iv Optimal stocking rate animal ha of total grasslands The name of this file is created from the name of the management file for automatic grazing by adding _inn at the end e g site1_year1 management_graz_inn dat Repeat these two steps for the following year year2 by replacing year1 by year2 and by specifying Restart files in PaSim run files For automatic cutting e RESTART_FILE_IN restart_site1_year1_cut txt e RESTART_ FILE OUT restart_site1_year2_cut txt For automatic grazing e RESTART FILE _ IN restart_site1_year1_graz txt e RESTART FILE OUT restart_site1_year2_graz txt You may imagine to simulate more than two successive years 34 35 2 3 3 Modelling C and C cycles with PaSim PaSim can be used to simulate the dynamics of 2 radioactive isotopes of the carbon in addition to the C C and C In order to do this the user has to Create a meteorological file for the considered isotope in Bq kg C for C or in for C like other meteorological files Note that only one of the isotopes can be simulated at the time Add
81. s not change 4 0 which canopy is half the maximum cannopy height Clover fraction kg kg Soil depth below which there is neither plant N m 0 2 uptake nor soil texture effect of active SOM decomposition Initial condition of shoot dry matter kg m Initial condition of root dry matter kg m Initial condition of LAI m laminae m 1 Initial cond for plant C substrate concentration kg C kg Prefer default value 0 04 Initial cond for plant N substrate concentration kg N kg Prefer default value 0 002 Initial cond for N conc of structural plant dry kg N kg Prefer default value 0 022 matter Relative root dry matter in different soil layers fraction Sum of all layers has to be 1 Shoot dry matter after cutting kg DM m 10 values LAI after cutting m laminae m 10 values Table 6 the plant tab parameters 39 3 2 The plant tab PaSim Laqueuille_int File Run Results Mode Overview Pla Maximal canopy height m 06 Initial condition of shoot dry matter kg m2 0 12 Canopy height parameter m En Initial condition of root dry matter kg m os Clover Fraction kg kg 012 Initial condition of LAI m2 leaf m2 Ho Soil depth below which there Initial cond for plant substrate kg C kg 0 04 is neither plant N uptake nor soil texture effect of Initial cond for plant N substrate kg N kg active SOM decomposition m 02 ER 2 0020 Initial cond for N conc of structural plant dry
82. ses from denitrification kg N m 2 7 n2oemissionsum n20 emission kg N m 2 7 69 n2oleachingS annual nitrous oxide leaching kg N m 2 7 namm ammonium n in soil layer h kg N m 2 2 namm_1 N ammonium in first soil layer kg N m 2 7 namm_2 N ammonium in second soil layer kg N m 2 7 namm_3 N ammonium in third soil layer kg N m 2 7 namm_4 N ammonium in fourth soil layer kg N m 2 7 namm_5 N ammonium in fifth soil layer kg N m 2 7 namm_6 N ammonium in sixth soil layer kgN m 2 7 nammsurface ammonium n at the soil surface kg N m 2 7 nammtot total N ammonium in soil kg N m 2 7 nanimaltot stocking rate animal m 2 7 napo n concentration of apoplast kg N m 2 7 NBP Net Biome productivity kg C m 2 7 ncuticle nh3 n auf der blattoberflaeche kg N m 2 7 NDF_total fraction of fibres in shoot 7 NDF fraction of fibres in the intake 7 NDFear Fraction of fibres in ingested ears 7 NDFlam Fraction of fibres in ingested lams 7 NDFstem Fraction of fibres in ingested sheaths and stems 7 NEE Net Ecosystem Exchange kg C m2 9 NEByoung Net energy balance of young or primiparous cows MJ 7 NEBmature Net energy balance of mature or multiparous cows MJ 7 NElyoung Net energy intake of young or primiparous cows MJ 7 NElmature Net energy intake of mature or multiparous cows MJ 7 nel net energy for lactation MJ kg 1 7 nelgrazingsum annual energy available for the whole cattle from grazing MJ kg 1 7 nfertammtot total N a
83. ses the carbon 14 specific interface he also has to load the carbon 14 file 44 VARIABLE DESCRIPTION UNIT Tcut Date of cutting event Julian day Tfert Date of fertilization event Julian day Nfertamm Amount of N ammonium for each kg N m application of mineral fertilizer Nfertnit Amount of N nitrates for each kg N m application of mineral fertilizer Nliqmanure amount of N in liquid manure kg Nm Nslurry amount of N in slurry kg Nm Nsolmanure amount of N in solid manure kg Nm Table 9 the cut and fert tab parameters 45 3 5 The Cut and Fert tab ES PaSim Laqueuille_int File Run Results Mode Overview Plant Soil Meteo Cut amp Fert Animal OutPuts Properties Number of management years 8 Cutting event Julian days Fertilization event Julian days 2 500 tes Amount of ammonium for each application of mineral Fertilizer kg N m2 Year o 2 0 0 0 00435 0 00345 0 00335 E 0 00355 i Amount of N in liquid manure kg M m2 Amount of N in slurry kg Nim Figure 12 Cut and Fert tab of the graphical interface This tab allows the user to define the cutting and fertilization events The number of management years is define in this tab and also affects the next tab Animal 46 VARIABLE UNIT HELP ADVISED
84. shoot structural dry matter kg m 2 9 stem component age 2 of shoot structural dry matter kg m 2 9 stem component age 3 of shoot structural dry matter kg m 2 9 stem component age 4 of shoot structural dry matter kg m 2 9 year y 8 carbon yield kg C m 2 9 nitrogen yield kg N m 2 7 maximal soil depth m 2 73 Annexe 4 restart file of PaSim restart txt version without C If you wish to modify the restart file manually take care to the number of characters N CONOR ND PaSim westructlignin nn2o 1 nn20 2 nn20 3 nn20 4 nn2o 5 nn2o 6 namm 1 namm 2 namm 3 namm 4 namm 5 namm 6 nnit 1 nnit 2 nnit 3 nnit 4 nnit 5 nnit 6 nammsurface wcactive wnactive wcstruct ncuticle wcmetabolic wnmetabolic wcslow wnslow wcpassive wnpassive wc wnapo wnsym wgn wlam 1 wlam 2 wlam 3 wlam 4 wear 1 wear 2 wear 3 wear 4 wst 1 wst 2 wst 3 Variables Carbon in the lignin of the structural dead dry matter N20 in soil layer 1 N20 in soil layer 2 N20 in soil layer 3 N20 in soil layer 4 N20 in soil layer 5 N20 in soil layer 6 Ammonium in soil layer 1 Ammonium in soil layer 2 Ammonium in soil layer 3 Ammonium in soil layer 4 Ammonium in soil layer 5 Ammonium in soil layer 6 Nitrate in soil layer 1 Nitrate in soil layer 2 Nitrate in soil layer 3 Nitrate in soil layer 4 Nitrate in soil layer 5 Nitrate in soil layer 6 ammonium in soil surface layer Carbon in active fr
85. soil organic carbon equilibrium Environmental Modelling amp Software In Press Riedo M Grub A Rosset M Fuhrer J 1998 A pasture simulation model for dry matter production and fluxes of carbon nitrogen water and energy Ecol Model 105 41 183 Riedo M Gyalistras D Fuhrer J 2000 Net primary production and carbon stocks in differently managed grasslands simulation of site specific sensitivity to an increase in atmospheric CO2 and to climate change Ecol Model 134 207 227 Riedo M Gyalistras D Fischlin A and Fuhrer J 1999 Using an ecosystem model linked with GCM derived local weather scenarios to analyse effects of climate change and elevated CO2 on dry matter production and partitioning and water use in temperate managed grasslands Global Change Biol 5 213 223 Riedo M Gyalistras D and Fuhrer J 2000 Net primary production and carbon stocks in differently managed grasslands simulation of site specific sensitivity to an increase in atmospheric CO2 and to climate change Ecol Model 134 207 227 Riedo M Gyalistras D and Fuhrer J 2001 Pasture responses to elevated temperature and doubled CO2 concentration assessing the spatial pattern across an alpine landscape Clim Res 17 19 31 Riedo M Milford C Schmid M and Sutton M A 2002 Coupling soil plant atmosphere exchange of ammonia with ecosystem functioning in grasslands Ecol Model 158 83 110 Schmid M Neftel
86. t activates trampling impact on vegetation 1 turnover FLAG_PLOUGHING Option that activates tillage effect on SOM mineralization Put 0 for permanent grassland and 1 for 0 If activated do not forget to adjust sown grasslands In the latter case you also PARAM_FREQ_PLOUGHING have to specify the tillage frequency DYN_LEGUME Actives legume dynamic Should be kept to 0 as not operational in 0 this version FLAG_IRRIGATION When activated the model will manage irrigation to satisfy 0 canopy water needs on the basis on water stress index FLAG_FERTILIZATION When activated the model will manage mineral nitrogen 0 fertilization to satisfy canopy nitrogen needs on the basis of nitrogen nutrition index FLAG_AUTOGESTION When activated mowing when set to 1 or grazing when This option is used for stocking rate and 0 set to 2 is managed by the model grazing coverage optimization at the forage system scale on one meteorological cycle FLAG_AUTOGESTION 2 implies iterative runs on each meteorological cycle FLAG_SATURANT Needed for auto management of Vuichard et al 2007 Should not be used anymore 0 FLAG_NONLIMITANT Needed for auto management of Vuichard et al 2007 Should not be used anymore 0 FLAG_COMPLEMENTATION 0 No supplementation This feature is still in implementation and 0 1 Prescribed forage supplementation not validated yet and so should not be used 2 Prescribed concentrate supplementation yet 3 Prescribed forage and concentrate
87. t have 4 columns e Year number 1 for the first year of simulation e Day Julian day from 1 to 365 PaSim do not consider bissextile year e Hour 1 to 24 e Climate variable of the file 2 1 1 1 2 Daily meteorological data PaSim offers the possibility to use daily meteorological data However note that using daily meteorological data instead of hourly meteorological data will reduce result precision To use daily meteorological data you will have to set the FLAG_READ_METEO flag to 1 into the site pasim file All meteorological Tab 1 data need to be aggregated into one file in the following order e Year Day Daily max temperature Daily min temperature Daily precipitation Daily Radiation Relative humidity Daily mean Wind speed Daily mean CO concentration Daily mean NH atmospheric concentration 12 VARIABLE Tcut Tfert Nfertamm Nfertnit Nanimal Tanimal Danimal Nliqmanure Nslurry Nsolmanure LWYcows LWMcows BCSYcows BCSMcows LWcalves AGE cow P AGE _cow M Forage quantity DESCRIPTION Date of a cutting event Date of a fertilization event Amount of N ammonium for each application of mineral fertilizer Amount of N nitrates for each application of mineral fertilizer Stocking rate Start of the grazing period Length of the grazing period Amount of N for each application of liquid manure Amount of N for each application of slurry Amount of N for each application of solid manure Initial average liveweig
88. tent on root and shoot turnover rates 7 gamsh_ear_1 total with senescence term turnover rate of ear compartment of age 1 d 1 7 gamsh_ear_2 total with senescence term turnover rate of ear compartment of age 2 d 1 7 gamsh_ear_3 total with senescence term turnover rate of ear compartment of age 3 d 1 7 gamsh_ear_4 total with senescence term turnover rate of ear compartment of age 4 d 1 7 gamsh_lam_1 total with senescence term turnover rate of lam compartment of age 1 d 1 7 gamsh_lam_2 _ total with senescence term turnover rate of lam compartment of age 2 d 1 7 gamsh_lam_3 total with senescence term turnover rate of lam compartment of age 3 d 1 7 gamsh_lam_4 total with senescence term turnover rate of lam compartment of age 4 d 1 7 4 4 4 4 ee gy ote gamsh_stem_1 total with senescence term turnover rate of stem compartment of age 1 d 1 7 gamsh_stem_2 total with senescence term turnover rate of stem compartment of age 2 d 1 7 gamsh_stem_3 total with senescence term turnover rate of stem compartment of age 3 d 1 7 gamsh_stem_4 total with senescence term turnover rate of stem compartment of age 4 d 1 7 gamshtot total senescent shoot dry matter kg DM m 2 7 gcrsum annual carbon substrate in root dry matter kg C kg DM 1 9 gcshsum annual carbon substrate in shoot dry matter kg C kg DM 1 9 gmean mean growth rate kg DM m 2 d 5 gpp gross primary productivity GPP kg C m 2 9 gr root growth rate kg m 2 d 1 9
89. testing tss 8 t_litter temperature of the litter K 7 turno_ra_ear1 senescence term wich accelerates the turnover of ear compartment of age 1 d 1 turno_ra_ear2 senescence term wich accelerates the turnover of ear compartment of age 2 d 1 1 7 7 turno_ra_ear3 senescence term wich accelerates the turnover of ear compartment of age 3 d 1 7 7 turno_ra_ear4 senescence term wich accelerates the turnover of ear compartment of age 4 d 1 turno_ra_lami senescence term wich accelerates the turnover of lam compartment of age 1 d 1 7 turno_ra_lam2 senescence term wich accelerates the turnover of lam compartment of age 2 d 1 7 turno_ra_lam3 senescence term wich accelerates the turnover of lam compartment of age 3 d 1 7 turno_ra_lam4 senescence term wich accelerates the turnover of lam compartment of age 4 d 1 7 turno_ra_stm1 senescence term wich accelerates the turnover of stem compartment of age 1 d 1 turno_ra_stm2 senescence term wich accelerates the turnover of stem compartment of age 2 d turno_ra_stm3 senescence term wich accelerates the turnover of stem compartment of age 3 d turno_ra_stm4 senescence term wich accelerates the turnover of stem compartment of age 4 d 1 u wind speed at reference height z above the canopy m s 7 un daily nitrogen uptake rate by the root kg N m 2 d 7 unamm N ammonium uptake rate of the root kg N m 2 d 7 unnit N nitrate uptake rate of the root kg N m 2 d 1 7 unsum nitrogen uptake rate of th
90. the location of this meteorological file in the names input file just after the path of the basic CO2 file Specify FLAG_ISOTOPE value in the PaSim run file o FLAG_ISOTOPE 0 only C o FLAG_ISOTOPE 1 C and C o FLAG _ISOTOPE 2 C and C Possibly add FLAG_DISINTEGRATION 1 in the PaSim run file if you want to activate disintegration only for C When simulating C and C cycles the structure of the restart file will change see Annexe 5 36 37 3 Graphical User Interface It is possible to use PaSim with its graphical interface It allows the user to create or to modify files needed for a simulation It also allows to run PaSim and to have results in an xls file In this interface there are eight tabs or nine if the user wants to use the sensibility analyse interface The six first tabs correspond to a specific part of the grassland properties such as the soil or the animals The two others tabs are related to PaSim the user can choose which outputs he wants with a graphic or not and select the properties of the simulation All of this will be explain in the following sections In order to help the creation of grassland a default value is proposed for most of the parameters the user has to fill These values are the advised values present in the tables of this user guide In each tab there is a valid button which allows the user to save and to check the integrity of the values he fills There is a
91. the pasimvar file HISTORY_NAME Variables chosen among the pasimvar file list Each name must be separated by one space not more no tabulation HISTORY Path and name of the output file HISTORY_WRT_FREQ Frequency of variable output s 86400 for a daily frequency 86400 HISTORY_CALC_FREQ Frequency of variable calculation s Better keep the reference value 1728 HISTORY_CALCUL Specify how the variable is calculated It must be specified for each of the output For example if you have chosen a daily frequency of variables Each output criteria must be variable output PaSim will output i the variable at the separated by one space not more no end of the day if NONE ii the daily average variable if tabulation AVE and iii the daily cumulated variable if SUM WRITE ALL for all the simulated years to be written in the output Choosing LAST_TURN for SOM file or LAST TURN for only the last year output values equilibrium simulations allows gaining time in the output file SORTIE Output format ASCII or NETCDF NETCDF format is used for spatial ASCII simulations DENITRIF Option that activates denitrification Must be 1 1 FLAG_LAISTRESS Option that activates limitation of vegetation turnover 1 rates driven by Leaf Area Index LAI FLAG_WATERSTRESS Option that activates water limitation effect on vegetation 1 age dynamics turnover FLAG_AGESTRESS Age dependent senescence 1 FLAG_MORTAGRAZ Option tha
92. ve traces in milk and meat products 1 3 Model evaluation All previous improvements have been evaluated against experimental data In particular PaSim was tested against experimental data at three European sites performing CO2 N20 and CH flux measurements Vuichard et al 2007 a PaSim has been used intensively in a set of European CarboEurope IP NitroEurope IP CARBO Extreme and French CLIMATOR VALIDATE research projects The model needs to be assessed as regards CH emissions for suckler and dairy cows either supplemented or not 1 4 Validity domain Based on previous studies Riedo et al 1998 Vuichard et al 2007a b and unpublished data the validity domain of the model corresponds to European soil climate conditions Permanent and sown grasslands Suckling and dairy pasture based seasonal calving systems French cattle breeds Prim Holstein Montb liarde Normande Charolais Salers 1 5 Modelling limitations Despite its continuous development and improvement some limitations remain e Vegetation PaSim representation of vegetation uses a compartment based approach neglecting i the spatial heterogeneity in paddocks diversity of plant populations of species and of cultivars ii almost fully the functional role of plant diversity e Soil PaSim representation of soil uses does not account for i soil atmosphere CH4 exchange ii the heterogeneous nature of the vertical distribution of C in the soil
93. wth for plant layer 1 kg m d 143 gmean2 Average growth rate during regrowth for plant layer 2 kg m d 144 gmean 3 Average growth rate during regrowth for plant layer 3 kg m d 145 gmean 4 Average growth rate during regrowth for plant layer 4 kg m d 146 gmean5 Average growth rate during regrowth for plant layer 5 kg m d 147 gmean 6 Average growth rate during regrowth for plant layer 6 kg m d 148 gmean 7 Average growth rate during regrowth for plant layer 7 kg m d 149 gmean 8 Average growth rate during regrowth for plant layer 8 kg m d 150 gmean 9 Average growth rate during regrowth for plant layer 9 kg m d 151 gmean 10 Average growth rate during regrowth for plant layer 10 kg m d 152 nfertammundissolved_inter Total ammonium dissolved from first time step Kg N m 153 nfertnitundissolved_inter Total nitrate dissolved from first time step Kg N m 154 kt 1 Thermal conductivity of layer 1 Int r t W m K 155 kt2 Thermal conductivity of layer 2 W m K 156 kt3 Thermal conductivity of layer 3 W m K 157 kt4 Thermal conductivity of layer 4 W m K 158 kt5 Thermal conductivity of layer 5 W m K 159 kt6 Thermal conductivity of layer 6 W m K 160 tsoilom Average temperature of lower boundary layer K 161 lecs 1 Water extracted by the root for the layer 1 mm 162 lecs 2 Water extracted by the root for the layer 2 mm 163 lecs 3 Water extracted by the root for the layer 3 mm 164 lecs 4 Water extracted by the root for the layer 4 mm 165 lecs 5 Water extracted by the ro

Pasim User Guide.pasim_v5.3_dec_2012

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