CARAIB USER'S GUIDE - ORBi
Contents
1. 3 4 3 Subroutines The following table lists all subroutines that are used in the model and written in caraib f The reader is referred to the code to look into details what these routines do Subroutine name Short description backdiff drv bashfor stept drv y ynew cal_in calrapportprecip zone month r rapportprecip charlen name kn check stept time y drv clasparam close_file iread correction crops seas ctgen cth20 daily weather drainage stept dryseas p mdry esat tk es exch ne nc je sl diag fire frac_herbs ngt frac_trees ngt funcx x fx gauss ne sl x generator graine iprint givedrv stept time y drv givnletters z nlet gpp cal hourly humiseas p mwet init c y ngt initbdo CARAIB USER s GUIDE 1 0 Computes back differences Linear multistep Adams bashforth method Calculates the external conditions at an hourly time step Calculates the value of precipitation ratio Counts the number of letters in a character 80 variable Arranges variables Reads or computes various age classes parameters Close all output files Used in fire Reads or computes various age classes parameters Reads constants for weather generator and sets them in commons Reads constants and sets them in commons Estimates daily weather data from monthly values Calculates the drainage Used in koppen2 Calculates saturation vapour pressure of H20 Exchanges rows to get a zero coefficient off the diagonal2. CARAIB USER S GUIDE version 1 0 CARAIB USER s GUIDE 1 0 Prepared by Julien Minet Ingrid Jacquemin Prof Louis Francois Universit de Li ge July 2013 Universit de Li ge SEPTEMBER 2013 1 Table of Contents ee IL DEE PT torva vec d gu tut Nu e UR nude LE DRM Em a ct 3 2 Theoretical CONCEP a eet t aad 3 2 T M in Ree e 3 22 Carbon and Ae 4 2 3 Evolution and CoimpetltiOn c eoe toner ea etui atl usa ta ean eo sheet dansscnusenseeletseleensauncieesies 4 2 4 Plant types characteristics and presence 4 GREEN Ee A 3 Code inputsand OMPI ias 4 AND A A er 4 3 2 Description of Inp r S AAA AAA A 5 3 2 1 The configuration file cra datada 5 Inputs parameters e Adone nn E 7 b Paths for Input a 8 C Paths Tor QUIDOC EE 9 d Lines for the years of sumulation eet de ces re oret etse rea a dou sene eer ero eee 9 3 2 2 Environmental input file eco dat ses 9 32209 C matre put EE 9 3 2 4 Plant parameters input Tiles a eripe Meet 10 3 3 Description of output Eeer A tu ere 13 34 Description or tie cod ue oret epe rere et DO E E pP uta eer potett 16 34 1 Pseudocode e a 16 3 4 2 Frequently used Varia DIS aee A voe DR epa i ater 17 Ee 17 A Technical Bri e 19 4 1 Compilation and EE 19 SAA ni CT 19 6 List ER Er bits 19 Reference Minet J Jacquemin I amp Fran ois L CARAIB user s
3. maritimus R obtusifolius R palustris R sanguineus R acetosella Trifolium alpestre T arvense T aureum T campestre T dubium T fragiferum T hybridum T medium T montanum T pratense T repens T spadiceum T striatum Petite oseille Tr fles 69
4. rectum C regelii runemarkii C scaposum C scaranii semidecandrum C siculum smolikanum C soleirolii C subtriflorum sylvaticum C thomasii C tomentosum transsilvanicum C uniflorum C vagans vourinense Holosteum umbellatum Moenchia erecta Myosoton aquaticum Stellaria calycantha S graminea S humifusa S longifolia S media S neglecta S nemorum S pallida S palustris Achyranthes Agriophyllum Alternanthera Amaranthus Anabasis Artrhocnemum Atriplex Axyris Bassia Beta Bienertia camphorosma Ceratocarpus Ceratoides GO 66000000290 O0000000000000000000 Populage des marais Cardamines Caryophyllac es C raistes Ch nopodiac es 65 Annexe 1 1 BAG Taxons palynologiques Taxons botaniques Noms vernaculaires 24 Chenopodium Cruciferae Polygonaceae Chenopodium Corispermum Cycloloma Girgensohnia Halimione Halimocnemis Halocnemum Halogeton Halopeplis Halostachys Hammada Kalidium Kochia Microcnemum Nanophyton Noaea Obione Ofaiston Petrosimonia Polycnemum Salicornia Salsola Suaeda Chenopodium acerifolium C album C ambrosioides C aristatum C bonus henricus C botryodes C botrys C exsuccum C ficifolium C foliosum C giganteum C glaucum C hybridum C jenissejense C multifidum C murale C opulifolium C polyspermum C pumilio C rubrum C schraderanum C suecicum C urbicum C v
5. Calculates probability of fire and burned area Used in npp cal Used in npp cal Numerical computation Solves a system of simultaneous linear algebraic equations by Gaussian elimination and back substitution Weather generator for precipitation and temperatures Runs the hydrological model Counts the number of letters in a character 8 variable Calculates the co2 net assimilation by leaves Arranges variables at an hourly time step Used in koppen2 Used in the hydrological model Numerical computation SEPTEMBER 2013 17 itochar2 i ch koppen2 climate lai_limit_w lailim_init mortality moulton stept drv y ynew new_frac ngt nonlineq xa xb nint x fx ermax nitmax imeth num npp cal ngt nyO iread ode tbegin tend y stept niter ipr open file iread open input5 nyrmax stept iread DI estab polfit xi yi ni aj ndeg err cj sl ponc_init printing ipr time y drv puiss x k xk randnum seed frnd read_cult ngt read_eco ngt read_in ngt read_init iread ngt record_grid y ngt remember drv runkut4 stept time y drv set_cpools ngt set_frac ngt soil_resp solar solar_flux solar_trees ngt tau aa bb fnet rdep drk0 X0 XN TAUI NI TDT mlength mondec flag tabrT tabrDT zone seed timedep stept time wat limit wri_1st y nyear ngt wri_res year_iteration zone2 reg region zonepxl2 iprint CARAIB USER S GUIDE 1 0 Convert an integer into a character Used in zonepxl2 Calculates monthly lai lim
6. Campanula Campanula cervicaria C glomerata Campanules C latifolia C patula C persicifolia C rapunculoides C rotundifolia C trachelium Cirsium Cirsium acaule C arvense C asculentum Cirses C heterophyllum C oleraceum C palustre C rhizocephalum C vulgare Epilobium Epilobium angustifolium E alsinifolium Epilobes E anagallidifolium E collinum E davuricum E hirsutum E lactiflorum E montanum E obscurum E palustre E parvifolium E roseum E tetragonum Filipendula Filipendula ulmaria F vulgaris Filipendules Galium Galium aparine G mollugo G odoratum Gaillets G palustre G pumilum G rotundifolium G saxatile G spurium G uliginosum G verum Geranium Geranium bohemicum G columbinum G raniums 25 G dissectum G lanuginosum G molle G palustre G pratense G pusillum G pyrenaicum G robertianum G sanguineum G silvaticum Geum Geum aleppicum G hispidum G rivale Benoites G urbanum Heracleum Heracleum sphondylium Berce sphondyle sphondylium Hippuris Hippuris tetraphylla H vulgaris Hippurides Pesses Melampyrum Melampyrum arvense M cristatum M lampyre M memorosum M polonicum M prater M sylvaticum Pedicularis Pedicularis flammea P lapponica P oederi P diculaire P palustris P sceptrum carolinum P sylvatica Rumex Rumex acetosa R acetosella R aquaticus Oseilles R acetosella Trifolium R conglomeratus R crispus R hydrolapathum R
7. Warnant P amp Munhoven G Modelling the glacial interglacial changes in the continental biosphere Global Planet Change 16 17 37 52 1998 e Francois L Y Godd ris P Warnant G Ramstein N de Noblet S Lorenz Carbon stocks and isotopic budgets of the terrestrial biosphere at mid Holocene and last glacial maximum times Chem Geol 159 163 189 1999 e Francois L M Ghislain D Otto A Micheels Late Miocene vegetation reconstruction with the CARAIB model Palaeogeogr Palaeoclim Palaeoecol 238 302 320 2006 e G rard J C Nemry B Francois L Warnant P The interannual change of atmospheric CO2 contribution of subtropical ecosystems Geophys Res Lett 26 243 246 1999 e Hajar L Frangois L Khater C Jomaa I D qu M Cheddadi R Cedrus libani A Rich CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 19 distribution in Lebanon Past present and future C R Biologies 333 622 630 2010 e Hubert B Francois L Warnant P amp Strivay D Stochastic generation of meteorological variables and effects on global models of water and carbon cycles in vegetation and soils J Hydrology 212 213 317 334 1998 e Laurent J M L Francois A Bar Hen L Bel R Cheddadi European Bioclimatic Affinity Groups data model comparisons Global Planet Change 61 28 40 2008 e Nemry B Fran ois L Warnant P Robinet F amp G rard J C The seasonality of the CO2 exchange between the atmosphere and the l
8. of plant types e Module Metabolic Structural fire ignition fine roots leaves wood lightning n Seed Dispersal l Short and long a distance CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 3 Deep drainage E gt 2 2 Carbon and water The present version of CARAIB includes two main modules 1 A hydrological module Improved Bucket Model IBM Hubert et al 1998 that calculates available soil water 2 A carbon module calculating carbon fluxes and pools in the biosphere Otto et al 2002 These two modules have been created separately This fact may induce discrepancies It is why an iteration is performed running the hydrological module and the carbon module for one complete year until their outputs became coherent steady state with equilibrium between water carbon cycle and vegetation distribution 2 3 Evolution and competition Simulations performed yet represent principally vegetation in equilibrium with climate but CARAIB was built to simulate also transient situations So even for steady state runs plants began as seeds and grow up until maturity Dispersion module is now implemented in CARAIB and competition for light and water are included Two strata of vegetation are simulated the first including principally trees and the second one concerning shrubs herbs and crops Competition for nutrient is only induced by C N dependent parameters The fraction of each pixel covered by a given Bioclimatic Affinity
9. prc dat oo AA H H MH GA AAA air temperature clim tem temp daily vari clim dte precipitation clim pre sunshine hour clim shr air relat humidity clim rhu wind speed clin wnd Lightning data clin lightning human coverage clim human frac path for generator gene PFT PFT PFT PFT PFT PFT tolerances parameters C N of veget 1 gkfall PFT gamai gama2 PFT carb_init Crops seasonality CARAIB USER S GUIDE 1 0 alb zzra t1 t2 age class para plantparam bagibm dat plantparam bagtol dat plantparam bagpar dat plantparam claspar dat plantparam csurn dat plantparam gkfall dat plantparam gama dat plantparam carbinit dat plantparam bagseas dat SEPTEMBER 2013 initial veget frac initial Min Max LAI read initial cond read lai limit in out climate zone in out stoch fields ibm results full 1st day of year res monthly lai limit results test file test problems current pixel date yearly mean results monthly mean sw monthly mean pet monthly mean aet monthly mean runoff monthly mean fsn monthly mean drain monthly mean vs ev monthly mean rbl monthly mean albedo monthly mean Rn monthly mean gr flx monthly mean Ts monthly mean fgs monthly mean LAI w month mean IRdown monthly mean H monthly mean LE monthly mean Fsol monthly mean sn fal monthly mean sn ev monthly mean sn mel monthly mean emisf monthly mean biom monthly m
10. Group BAG is calculated as being proportional to the BAG s Net Primary Productivity NPP 2 4 Plant types characteristics and presence Vegetation is distributed in 26 BAGs Laurent et al 2004 representing both the functional type and the adaptation to climate The example version of CARAIB also includes 8 plant species for which carbon pools and fluxes are calculated separately the results here are not included in pixel means In the newest versions CARAIB does also include crops 2 5 References See at this end of the document for a alphabetic list of references related to CARAIB The most comprehensive and first reference is the PhD thesis of Pierre Warnant ULg 1999 written in French Alongside with this document is the paper describing the model and its first application to the global scale Warnant et al 1994 The soil respiration mechanisms were introduced by Nemry et al 1996 Hubert et al 1998 latter improved the description of the hydrological processes using a new hydrological model called the Improved Bucket Model IBM Then Otto et al 2002 improved the model by introducing two vegetation storeys respectively trees and herbs amp shrubs Lastly a fire module simulating the occurrence and the propagation of fires was introduced by Dury et al 2011 3 Code inputs and outputs 3 1 Directory tree All the code is gathered in a directory with files and subdirectories which are the following e caraib f For
11. P Monthly or daily values of evapotranspiration Monthly or daily probability of fire Monthly or daily values of aerodynamic resistance for water averaged over vegetation and soil potential Ratio of minimal LAI over maximal LAI per BAG Monthly or daily values of mean net radiation Monthly or daily values of runoff Monthly or daily values of the snow fall Monthly or daily values of the snow melt Monthly or daily values of the snow evaporation Monthly or daily values of soil vegetation evapotranspiration It includes all evapotranspiration except snow evaporation and evaporation of intercepted water Monthly or daily values of soil moisture Expressed in relative units such as it equals O at the wilting point 1 at the field capacity and is superior to1 beyond field capacity and saturation Yearly minimal and maximal daily temperature Yearly minimal and maximal monthly temperature month average Monthly or daily values of the temperature of the surface Yearly water budget for each pixel This file summarizes all components of the water budget over a year The following parameter are written Pixel number igr longitude ylongi latitude ylati water height at saturation mm fsi water height at field capacity mm fci water height at wilting point mm wpi root depth mm rootd Annual sum of precipitation mm prcy Sum of runoff mm runy Sum of evapotranspiration mm
12. P macrosepala P polygonifolia P pontica P rechingeri P rouyana P suffruticosa P taurica Plantago lanceolata Plantago lanceolata Plantain lanc ol Polygonum aviculare Polygonum aviculare Renou e des oiseaux P bistorta P bistorta Renou e bistorte P persicaria P hydropiper P lapathifolium P minus Renou e persicaire P mite P persicaria 21 Sanguisorba Sanguisorba officinalis S minor Sanguisorbe S minor S minor Petite pimprenelle S officinalis S officinalis Pimprenelle officinale Saxifraga Saxifraga adscendens S aizoides Saxifrages S cernua S cespitosa S cotyledon S granulata S hirculus S oppositifolia S rivularis S stellaris S tridactylites f S aizoides S aizoides Saxifrage faux aizoon Scleranthus Scleranthus annus S perennis S uncinatus Scl ranthe Polycarpon diphyllum P tetraphyllum Spergula Spergula arvensis S morisonii S pentandra SPergule Succisa pratensis Urtica Urticaceae S viscosa Spergularia echinosperma S maritima S rubra S rupicola S salina S segetalis Succisa pratensis Urtica atrovirens U dioica U kioviensis U membranacea U morifolia U pilulifera U rupestris U urens Forsskalea Parietaria Soleirolia Urtica Succise des pr s Orties Urticac es 62 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Asteraceae Achillea Adenostyles Andryala Antennaria Asteroi
13. agtol dat iPFT BAG s number ic4 1 for CA plant else 0 idec 1 for deciduous plan else 0 tmin1 Minimum threshold for stress pool 1 SE tmin2 Minimum threshold for stress pool 2 C tmax1 Maximum threshold for stress pool 1 C tmax2 Maximum threshold for stress pool 2 C watl Soil water content expressed as a fraction of field capacity wat2 Soil water content expressed as a fraction of field capacity xparl Solar energy threshold MJ day xpar2 Solar energy threshold MJ day GDD5_min Minimum value of GDD base 5 C_ 2 C Tmax_germ Maximum temperature for germination C watmax_germ Maximum soil water content for germination pgerm Germination probability bag_h jbbag Quantile carbinit dat carb_init pool N Initial value of carbon pool pool 1 gC m Carb init pool N Initial value of carbon pool pool 2 gC m claspar dat nclas Number of age classes for this BAG nclas values Follow up of the age classes for this BAG iyear max Lifespan max year csurn dat csurn C N ratio for this BAG pool 1 96 pool N C N ratio for this BAG pool 2 96 CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 12 gama dat gamal pool N 1 Fraction allocated to green litter gamal pool N 2 Fraction allocated to not green litter gama2 Fraction integrating the soil organic carbon rest in the atmosphere gkfall dat 1 gkfall 4 values for the mortality characteristic time without or with year stress and for pool 1 and poo
14. al wood pools csurn dat Path for the parameter file of characteristic times of leaves fall and wood dead gkfall dat Path for the parameter file of multiplying factor for litter y1 and soil carbon y2 decomposition gama dat Path for the parameter file of carbon content of seed carbinit dat SEPTEMBER 2013 8 Crops seasonality Path for the parameter file of crop phenology parameters bagseas dat c Paths for output files The following lines set the paths of the output files of the simulation results Most of these paths refer to a set of files with one file per year following the format temYEAR dat with YEAR being the year e g sw2012 dat The output files can be written or not depending on the flag number that is written between the results name and the path name of the output file with this number equals to 1 or 0 for writing and not writing respectively For instance the following line tells CARAIB to write the results of soil water to the file swYEAR dat monthly mean sw 1 results sw The paths are not detailed here Please refer to the configuration file caraib dat printed out above in this document The content of the output files are fully described in another section below d Lines for the years of simulation The last lines of the configuration file caraib dat are for the years of simulation The first column is an ordinary list of the years from 1 to the number of years The second c
15. and biosphere a study with a global mechanistic vegetation model J Geophys Res 101 7111 7125 1996 e Nemry B L Francois J C G rard A Bondeau M Heimann Comparing global models of terrestrial net primary productivity NPP analysis of the seasonal atmospheric CO2 signal Global Change Biology 5 Suppl 1 65 76 1999 e Otto D D Rasse J Kaplan P Warnant L Francois Biospheric carbon stocks reconstructed at the Last Glacial Maximum comparison between general circulation models using prescribed and computed sea surface temperatures Global Planet Change 33 117 138 2002 e Warnant P Francois L Strivay D G rard J C CARAIB a global model of terrestrial biological productivity Global Biogeochemical Cycles 8 255 270 1994 e Warnant P 1999 Mod lisation du cycle du carbone dans la biosph re continentale l chelle globale PhD thesis Universit de Li ge Li ge Belgium e Zobler L A 1986 A world soil file for global climate modeling NASA technical memorandum 87802 NASA Goddard Institut for Space Studies GISS New York CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 20 Annexe 1 1 Attribution des taxons palynologiques aux Groupes Affinit s Bioclimatiques ou Bioclimatic Affinity Groups BAG Correspondances entre taxonomie palynologique botanique et appellations vernaculaires Les appellations botaniques sont celles de l Atlas Florae Europaeae Jalas amp Suominen 1972 1994 Jalas
16. ara C asarifolia C bellidifolia bulbifera C caldeirarum C carnosa chelidonia C corymbosa C crassifolia enneaphyllos C flexuosa C glanduligera glauca C gracea C granulosa heptaphylla C hirsuta C impatiens kitaibelii C macrophylla C majovskii maritima C montelucii C nymanii parviflora C pentaphyllos C plumieri pratensis C quinquefolia C raphanifolia schulzii C tenera C trifida C trifolia udicola C uliginosa C waldsteinii Agrostemma Arenaria Bolanthus Bufonia Cerastium Chaetonychia Corrigiola Cucubalus Cyathophylla Dianthus Drypis Gypsophila Hernaria Holosteum Honkenya lllecebrum Loeflingia Lychnis Minuartia Moehringia Moenchia Myosoton Ortegia Paronychia Petrocoptis Petrorhagia Polycarpon Pseudostellaria Pteranthus Sagina Saponaria Scleranthus Silene Spergula Spegularia Stellaria Telephium Vaccaria Velezia Cerastium alpinum C alsinifolium arcticum C arvense C azoricum banaticum C biebersteinii brachypetalum C candidissimum carinthiacum C cerastoides dahuricum C decalvans C dichotomum diffusum C dinaricum C dubium fontanum C gibraltaricum C glabratum glomeratum C gracile C grandiflorum illyricum C jenisejense C julicum latifolium C ligusticum C lineare maximum C moesiacum C nemorale pauciflorum C pedunculare pedunculatum C perfoliatum C pumillum pyrenaicum C
17. ca S caesia S caprea S caspica S cinerea S crataegifolia S daphnoides S eleagnos S foetida S fragilis S glabra S glauca S glaucosericea S hastata 13 S hegetschweileri S helvetica S herbacea S hibernica S jenisseensis S kitaibeliana S laggeri S lanata S lapponum S mielichhoferi S myrsinifolia S myrsinites S myrtilloides S nummularia S pedicellata S pentanara S phylicifolia S polaris S pulchra S purpurea S pyrenaica S pyrolifolia S recurvigemmis S repens S reptans S reticulata S retusa S rosmarinifolia S serpillifolia S silesiaca S starkeana S tarraconensis S triandra S viminalis S vinogradovii S waldsteiniana S wilhelmsiana S xerophila Cistus Cistus albidus C monspeliensis Cistes 14 C salviaefolium Myrtus Myrtus communis Myrte Buxus sempervirens Buxus sempervirens Buis Hedera helix Hedera helix Li re 15 Ilex aquifolium Illex aquifolium Houx Ligustrum vulgare Ligustrum vulgare Tro ne Viscum Viscum album V cruciatum Gui Arctostaphyllos uva Arctostaphyllos uva ursi Raisin d ours ursi 16 Calluna vulgaris Calluna vulgaris Bruy re commune Daphne Daphne mezereum Daphn s Berberis vulgaris Berberis vulgaris pine vinette Crataegus Crataegus calycina C laevigata Aub pines C monogyna Euonymus Euonymus europaeus Fusain d Europe 17 europaeus Genista Genista anglica G germanica G pilosa Gen ts G tinctoria Rhamnus Rhamnus alpi
18. d es 22 asteroideae Asteraceae cichorioideae Gramineae Myriophyllum Umbelliferae Arctium Arnica Arnoseris Artemisia Aster Bellis Bidens Buphthalum Calendula Carduncellus Carduus Carlina Carthamus Centaurea Chrysanthemum Cirsium Crupina Doronicum Echinops Erigeron Eupatorium Evax Filago Galactites Gnaphalium Helichrysum Inula Leuzea Matricaria Mycelis Pallenis Petasites Phagnalon Pulicaria Senecio Serratula Tussilago Catananche Chonarilla Cicerbita Cichorium Crepis Hedypnois Hieracium Homogyne Hyoseris Hypochoeris Lactuca Lagoseris Lapsana Leontodon Micropus Picris Prenanthes Reichardia Santolina Scolymus Scorzonera Solidago Sonchus Staehelina Traxacum Thrincia Tolpis Tragoporon Urospermum Agropyrum Agrostis Aira Alopecurus Ammophila Andropogon Anthoxantum Arrhenatherum Arundo Avellinia Avena Brachypodium Briza Bromus Calamagrostis Catapodium Corynephorus Cynodon Cynosurus Dactylis Danthonia Deschampsia Digitaria Echinochloa Elymus Festuca Gastridium Glyceria Holcus Hordeum Koelaria Lagurus Leersia Lepturus Lolium Melica Mibora Milium Molinia Nardurus Nardus Oryza Oryzopsis Paspalum Phalaris Phleum Poa Polypogon Psilurus Scleropoa Sesleria Setaria Sporobolus Stypa Trisetum Vulpia Myriophyllum alterniflorum M spicatum M verticillatum Aegopodium Aethusa Angelica Anthriscus Apium Astran
19. ditions in the model Not to be mistaken with human frac dat that refers to the fraction of land use see above xlai min max res 21 Initial Min Max LAI Minimal and maximal value for LAI values of the m m read if ilai_rd 1 BAGs that are modeled in CARAIDB First are the minimal values for all the BAG that are used then the maximal values for hydrological module biomass res read 25 Initial values Initial values for soil water content carbon in the if iread 1 two pools for bud litter and human frac ylailim res read 125 LAI limitation Initialisation of xImin and xlmax cf bagibm dat if iread 1 zone res read if 22 Determination of the climate zone for all pixels iczon 1 CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 13 stochas gen read 23 if ngener 1 water full open if 24 ifull 1 biomass 26 ylailim 126 water tes 28 carbon problem 61 water time 29 Daily results if ifull 1 Problem Initialisation of the weather generator calculation of different probabilities for the 176 climatic zones of Koppen Write sngl carbon content of pools parameter of the equation for available biomass for bud litter and humus values Write xlmin and xlmax cf bagibm dat Write calculation for average surface temperature Some error messages can be printed in this file The output files of the second group are detailed below in alphabetic order There are actually a set of files with one file per year following the forma
20. ean gpp monthly mean npp monthly mean nep monthly mean lai C veget cover frac annual npp plant Rmin Min Max LAI GPP Cveg Csoil C13 fractionation Mean LAI Tmin Tc GDD probability of fire burned pix fraction burned area daily species npp year pco2 iprt 1 380 1 2 380 1 CARAIB USER s GUIDE 1 0 A CO O OQ AAA Q B PH H HR B p pi ES ES ES AAA AA ES S EA ES ES S EA EA AA EA EA ES B ES ES E E EH results frac res results xlai min max res results biomass res results ylailim res results zone res results stochas gen results water full results biomass results ylailim results water tes results carbon problem results water time f 2 2 results water yr results sw results pet results aet results run results fsn results drn results sve results rbl results alb results rn results grf results ts results fgs results lai results fird results xh results xle results fsol results sf results sne results sml results emisf results biommth results gppmth results nppmth results nepmth results laimth results frac results npp results Rmin results xlai min max results gpp results Cveg results Csoil results frcC13 results laimoy results Tdmin results Tmmin results gdd results pfire results fburn results aburn results nppd ilexto must start in column 21 filexti mu
21. et al 1996 1999 et de I Atlas of North European vascular plants north of the Tropic of Cancer I II Hult n amp Fries 1986 La correspondance avec la taxonomie palynologique provient de Moore et al 1991 et de Punt et al 1994 Les noms vernaculaires sont issus de Rameau et al 1993 Annexe 1 1 BAG Taxons palynologiques Taxons botaniques Noms vernaculaires Cedrus C atlantica C libani C dres 1 Pinus halepensis Pinus halepensis Pin d Alep Pinus pinaster Pinus pinaster Pin maritime Abies alba A alba Sapin pectin Taxus Taxus baccata If commun Pinus cembra Pinus cembra Pin cembro Cupressaceae Cupressus Juniperus Tetraclinis Juniperus communis Juniperus communis Gen vrier commun B5 Abies A alba A borisii regis A cephalonica Sapins A nebrodensis A pinsapo A sibirica Picea Picea abies P omorika pic as Pinus Pinus brutia P cembra P halepensis Pins 6 P heldreichii P mugo P nigra P peuce P pinaster P pinea P sibirica P sylvestris P uncinata Pinus sylvestris Pinus sylvestris Pin sylvestre 7 Larix Larix decidua L sibirica M l zes Olea europaea Olea europaea Olivier Phillyrea Phillyrea Filaires 8 Pistacia Pistacia Pistachiers Quercus ilex Quercus coccifera Q ilex Ch ne vert Quercus suber Quercus suber Ch ne li ge Castanea Castanea sativa Ch taignier 9 Juglans Juglans regia Noyer Ostrya Ostrya carpinifolia Charme houblon Que
22. guide Universit de Li ge Li ge Belgium 2013 CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 2 1 Introduction CARAIB is a dynamic vegetation model DVM written in FORTRAN and developed at Universit de Liege It can simulate the vegetation growth from the local to the global scales for various crops and natural vegetation and has been applied for past and future ecosystems This is the first version of the CARAIB user s guide This guide is to help you making your first steps using the model CARAIDB It focuses on the description of the inputs and outputs files There are a brief description of the model as a pseudocode and a list of the routines used in the model 2 Theoretical concepts 2 1 Main structure CARAIDB is a mechanistic model studying vegetation behaviour as a function of climate and soil It is built to cover many time and spatial scales from local vegetation and diurnal cycle to global cover over centuries It is composed of several modules that were progressively added to the model The figure below presents the current modules of the model with their inter relationships CARAIB H 0 CO Dynamic Vegetation Model Photosynthesis Vegetation Hydrological Ecosystem Budget Stomatal C3 amp C4 plants Service Precptation Regulation Farquhar et al 1980 establishment Provision Collatz et al 1992 competition mortality of plant types Allocation Growth Respiration assemblage Fire
23. ha and the dry matter intake in kgC animal The units are to be considered on a monthly or a daily basis according to the user s choice idaily in 3 2 4 Plant parameters input files The input plant parameters files contain physiological data for each BAG that is defined in the model There are currently 25 BAG of natural vegetation and 9 cultivated crops The natural vegetation BAG can be classified in herbaceous vegetation BAG 21 25 shrubs BAG 14 20 and trees BAG 1 19 A full list of the species in each BAG can be found in Annex I BAG number Main species 25 Achillea Alchemilla Angelica Campanula 24 Brassicaceae Caltha Cardamine etc 23 Anthemis Artemisia Bidens Calystegia etc 22 Asteraceae asteroideae Poaceae etc 21 Anemone Gypsophila Helleborus etc 20 Ephedra Ulex 19 Alnus vir Arctostap A alpinus B nana CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 10 18 Sambucus Frangula a Prunus Sorbus Vaccinium 17 Berberis vul Crataegus Genista Rhamnus 16 Artostaphylos uva ursi Calluna vul Daphne 15 Buxus sempervirens Hedera h Ilex acquif 14 Cistus Myrtus 13 Betula Salix 12 Alnus A gl Corylus Q robur Populus Tilia 11 Acer Fraxinus F excel Tilia cordata Ulmus 10 Acer campestre Carpinus Fagus syl Tilia pla 9 Castanea Juglans Ostrya Q pubescens 8 Olea eur Pistacia Phillyrea Q ilex Q suber 7 Larix decidua 6 Picea abies Pinus Pinus sylvestris 5 Abies 4 Cup
24. inp weather fil ext results Spatial resolution degree which is equals to the product of the longitude by the latitude e g 0 25 for a simulation on a 0 5 X 0 5 grid in longitude latitude Eccentricity of Earth s orbit degree Earth s obliquity degree Longitude of perihelion of Earth s orbit degree Number of herbaceous BAGs Number of shrub BAGs Number of tree BAGs Number of crop BAGs Extension of the input files for weather Usually set to dat Extension of the output files Usually set to res b Paths for input files The following lines set the paths of the input files for environmental meteorological and plant physiology data The content of the input files are fully described in another section below Parameter name Description soil texture air temp climatol precip climatol air temperature temp daily vari precipitation sunshine hour air relat humidity wind speed lightning data human coverage path for generator PFT alb zzra t1 t2 PFT tolerances PFT parameters PFT age class para PFT C N of veget PFT 1 gkfall PFT gamal gama2 PFT carb_init CARAIB USER S GUIDE 1 0 Path for the soil texture parameters eco dat Path for the monthly or daily average air temperature data climatological values used to determine the pixel climatic type Path for the monthly or daily average precipitations data climatological values used to determine the pixel climatic
25. its to assure coherence between CARAIB and IBM Reads initial value of lai limitation due to water stress Calculates the mortality rate Linear multistep Adams bashforth method Calculates the vegetation succession Solves a non linear equation of the type Calculates the net primary productivity and the co2 carbon pools Resolves ordinary differential equations used in givedrv Open input and output files Open and read caraib dat Estimates establishment success for plant types Numerical computation Performs the initialisation of some variables ynpp ygpp ynep xmnpp xmgpp Zgpp Summarizes and writes some variables Numerical computation Returns a random number between 0 and 1 Reads the PFT fraction over the pixel Reads the different environmental inputs as well as vegetation characteristics Read environmental and vegetation inputs and compute some environmental parameters Reads initial conditions files Records soil water biomass soil carbon and leaf area index in vectors for initialisation at the beginning of the next year Saves the derivatives and back differences at previous time step Runge Kutta method Reads initial value of carbon pools and set them in the right form Reads the different environmental inputs as well as vegetation characteristics and sets them in the right form Estimates the monthly soil respiration rate Calculates the solar irradiance at the earth surface Calculates the radiative tran
26. ium Chrysosplenium alterniflorum Dorines C oppositifolium Gypsophila Gypsophila acutifolia G altissima G arrostii Gypsophiles G belorossica G bermejoi G collina G elegans G fastigiata G glomerata G linearifolia G litwinowii G macedonia 21 G montserratii G muralis G nana G pallasii G paniculata G papillosa G patrinii G perfoliata G petraea G pilosa G repens G scorzonerifolia G spergulifolia G struthium G tomentosa G uralensis Helleborus Helleborus bocconei H dumetorum Hell bores H foetidus H lividus H multifidus H niger H odorus H orientalis H purpurascens H viridis Hellianthemum Helianthemum nummularium H oelandicum H lianth mes Humulus Humulus lupulus H scandens Houblons Jasione montana Myrica Jasione montana Myrica faya M gale Jasione des montagnes Myrique 61 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Papaver Papaver alpinum P apulum P arenarium Pavots P argemone P chibinense P croceum P dahlianum P dubium P guerlekense P hybridum P laestadianum P lapeyrousianum P lapponicum P macrostomum P pinnatifidum P purpureomarginatum P radicatum P rhoeas P rupifragum P somniferum Paronychia Paronychia albanica P arabica Paronyque P aretioides P argentea P bornmuelleri P capitata P cephalotes P chionaea P echinulata P kapela P macedonica
27. l 2 1 gkboom Characteristic time for bud formation year bagseas dat sowing date Sowing date For crops only Set to 999 for the natural Julian day vegetation BAGs temp base Base temperature for the plants Does not apply for the natural C vegetation BAGs gdd_germ Sum of degrees days needed for germination C days gdd harv Sum of degrees days needed for harvest C days 3 3 Description of output files Output or results files are ASCII files For most of files the output data are on a daily or a monthly basis depending on the choice of the user parameter idaily_ou in caraib dat There is one line per simulated pixel Most of these files start with the longitude and latitude of the simulated pixel first two columns Hereafter is a description of all possible output files The file number refers to an identifier number in the code caraib f There are two groups of output files 1 output files that are printed and with one file for all years of simulations and 2 output files that are printed or not depending on the user s choice and with one file per year of simulation The output files of the first group are detailed below File File Parameter name Description Units number frac res read if 20 Vegetation fraction It is the fraction of each BAG for each pixel This ifrac_rd 1 file is actually an input file and output file as the BAG fraction can evolve following the dissemination of BAG depending on evolving climatic con
28. lchrum H tetrapterum Knautia arvensis Lamium album L amplexicaule L hybridum L moluccellifolium L purpureum Lysimachia nemorum L nummularia L thyrsifolia L vulgaris Lythrum portula L salicaria Argemone Capnoides Ceratocapnos Chelidonium Corydalis Dicentra Eschscholzia Fumaria Glaucium Hypecoum Meconopsis Papaver Platycapnos Pseudofumaria Roemeria Rupicapnos Sarcocapnos Plantago coronopus P indica P lanceolata P major P maritima P media P tenuiflora P major Polygala amarella P comosa P vulgaris Potentilla anglica P anserina P argentea P cinerea P collina P erecta P fructicosa P heptaphylla P norvegica P palustris P recta P reptans P rupestris P sterilis P tabenaemontani P thuringiaca Sedum acre S album S anglicum S annuum S reflexum S sexangulare S telephium S villosum Stachys arvensis S palustris S officinalis So Do Eo Co Oo lo Do Io Liseron des haies Chardons Euphorbes Millepertuis Knautie des bois Lamiers Lysimaques Pourpier et Salicaire Pavots Plantains Plantain larges feuilles Polygales Potentilles Orpins Epiaires 64 Annexe 1 1 BAG Taxons palynologiques Taxons botaniques Noms vernaculaires 24 Caltha Cardamine Caryophyllaceae Cerastium Chenopodiaceae Aquilegia vulgaris Caltha palustris Isopyrum thalictroides Myosurus minimus Cardamine am
29. lting in 12 or 365 more columns respectively For each meteorological variable there is a set of files with one file per year following the format filenameYEAR dat with YEAR being the year e g tem2012 dat is the input file for temperatures in 2012 File name Meteorological variable Units YEAR da tem Mean temperature C dte Daily amplitude of temperature Tmax Tmin C pre Precipitation mm shr Sunshine hours rhu Relative humidity wnd Wind speed m s lightning Rate of lightning flashes km human_frac Fraction of pixel area covered by the following 5 classes natural vegetation crops urban water bodies rocks The sum of the fractions must be equal to 1 manag Management file for the cutting of the biomass The first two columns are for the longitude and latitude The third column is the flag variable for enabling cutting 0 or 1 the fourth is the number of cuts during the year Then the following columns are the day of the year of the cutting the LAI after cutting Mm eaves M surface and the dry matter after cutting in gC m grazing Management file for the grazing of the biomass The first two columns are for the longitude and latitude The third column is the flag variable for enabling grazing 0 for nothing 1 for cutting and 10 for grazing the fourth is the number of grazing days during the year Then the following columns are the day of the year when grazing occurs the animal density in animal
30. naculaires 24 Polygonum Ranunculaceae Ranunculus Polygonum acetosum P alpinum UU UD UU UU amphibium P amplexicaule aschersonianum P aviculare P bistorta capitanum P cognatum P equisetiforme floribundum P foliosum P graminifolium humifusum P hydropiper hydropiperoides P icarium P idaeum lapathifolium P laxmanii P maritimum mesembricum P minus P mite P molle nepalense P orientale P oxyspermum P patulum P persicaria P polystachyum P P P romunum P sagittatum P salicifolium salsugineum P samarense P scoparium tenoreanum P viviparum Aconitum Actaea Adonis Anemone Aquilegia Callianthemum Caltha Ceratocephalus Cimicifuga Clematis Consolida Delphinium Eranthis Garidella Helleborus Hepatica Isopyrum Myosurus Nigella Pulsatilla Ranunculus Thalictrum Trollius Anemone nemorosa Clematis vitalba Pulsatilla vulgaris Ranunculus abnormis 2 2 D acetosellifolius R aconitifolius R acris aduncus R aesontinus R affinis allemannii R alpestris R amplexicaulis angulatus R appeninus R aquatilis arvensis R asiaticus R auricomo binatus R auricomus R auricomus VNVANADDADAADAAAANAAANAAAAAAAAAAAAAA barceloi R batrachioides R bilobus brevifolius R brutius R bulbosus bullatus R bupleuroides R cacuminis carinthiacus R carlittensis R carpaticus cassubicifolius R ca
31. nus R catharticus Nerpruns Rhamnus catharticus Rhamnus catharticus Nerprun purgatif Sambucus Sambucus nigra S racemosa Sureaux 60 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Frangula alnus Frangula alnus Bourdaine Lonicera Lonicera caerula L periclymenum L villosa Ch vrefeuilles L xylosteum Prunus Prunus avium P padus P spinosa Pruniers Rubus Rubus arcticus R caesius Ronces R chamaemorus R idaeus R plicatus 18 R saxatilis ER Sorbus Sorbus aria S aucuparia S hybrida Alisiers Sorbiers S intermedia S meinichii S obtusifolia S rupicola Vaccinium Vaccinium macrocarpum V microcarpum Myrtilles Airelles V myrtillus V oxycoccos V uliginosum V vitis idea Viburnum Viburnum opulus Viorne Alnus viridis Alnus viridis Aulnes vert Arctostaphyllos Arctostaphyllos alpinus A uva ursi Busserole Raisin d ours Arctostaphyllos Arctostaphyllos alpinus Busserole des Alpes 19 alpinus Betula nana Betula nana Bouleau nain Hippophae Hippophae rhamnoides Argousier rhamnoides 20 Ephedra Ephedra dystachya E fragilis E major Eph dre Ulex Ulex europaeus Ajoncs Anemone Anemone altaica A apennina A baldensis An mones A blanda A canadensis A coronaria A dichotoma A hortensis A narcissifolia A nemorosa A palmata A palvoniana A pavonina A ranunculoides A reflexa A sylvestris A trifolia A uralensis Chrysosplen
32. oid setting ifull to 1 except for test simulations performed on one single pixel 0 otherwise 1 to call the fire module 1 to print fire module results Total number of years 1 for steady state run or 1 year run more otherwise Iteration step in IBM 1 for normal run Number of years for which IBM results are printed Usually 1 Timestep of printing for IBM if ifull 1 0 to calculate initial value of soil water content and carbon content 1 to read it in biomass res and in ylailim res copied files from a previous simulations in directory results 1 to calculate climate type of each pixel otherwise read climate type in zone res 1 to read daily weather data in the climatic files 0 otherwise If set to 1 daily weather data must be available in the climatic input directory If set to 0 yearly weather data are used in combination with the weather generator to generate daily values 1 to write daily output in the results files 0 otherwise Number of pixel 1 We strongly recommend to make a steady state run with a timeserie composed of A repetition of a timeserie of reference to obtain by another way equilibrium for example 7 times the period 1960 to 1999 but noted at the end of caraib dat as a run between 1720 to 1999 Your timeserie over which you want run CARAIB for example 2000 to 2100 CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 7 resolution lg lt exc obl xlsper nherb nbush ntree nc fil ext
33. olumn pco2 is for the CO2 concentration in the atmosphere in ppm The third column iprt is to set the printing 1 or not 0 the results for that year The last two columns are for the file extension of the output files filexto and the input files filexti Those lines must be repeated for each year in a transient run while for a steady state simulation with climatological fields only one set of values one line is necessary 3 2 2 Environmental input file eco dat The input file eco dat holds information for each pixel about the physical characteristics of the simulated areas including geographic localisation soil type and soil texture There is one line per simulated pixel It contains 10 parameters arranged as columns that are Pixel number Longitude decimal degrees Latitude decimal degrees The FAO soil number determining each texture percentage Zobler 1986 Clay content in 96 Silt content in 96 Sand content in 96 Elevation above sea level m Soil color 0 is black 1 is white SA Fer s 3 2 3 Climatic input files The input climatic files contain meteorological data for each simulated pixel There is one line per simulated pixel All these files start with the longitude and latitude of the simulated pixel first two columns The data are on a monthly or a daily basis depending on the value of the input parameter CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 9 idaily in respectively O or 1 resu
34. rcus pubescens Quercus pubescens Ch ne pubescent Acer campestre Acer campestre rable champ tre 10 Carpinus Carpinus betulus C orientalis Charmes Fagus sylvatica Fagus sylvatica H tre Tilia platyphyllos Tilia platyphyllos Tilleul grandes feuilles Acer Acer platanoides rable plane Fraxinus Fraxinus excelsior F ornus F oxyphylla Fr nes 11 Tilia cordata Tilia cordata Tilleul petites feuilles Ulmus Ulmus glabra U laevis U minor Zelkova Ormes abelicea Alnus Alnus cordata A glutinosa A incana Aulnes A viridis Alnus glutinosa Alnus glutinosa Aulne glutineux Corylus avellana Corylus avellana Coudrier Quercus Quercus canariensis Q cerris Q congesta Ch nes Q crenata Q faginea Q frainetto 12 Q fructicosa Q hartwissiana Q macrolepis Quercus robur Populus Tilia Q pedunculiflora Q petraea Q pubescens Q pyrenaica Q robur Q rotundifolia Q sicula Q trojana Quercus robur Populus alba P canescens P nigra P tremula Tilia cordata T platyphyllos Ch ne p doncul Peupliers Tilleuls 59 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Betula Betula humilis B nana B pendula Bouleaux B pubescens Salix Salix acutifolia S aegyptiaca S alba Saules S alpina S amplexicaulis S appendiculata S appenina S arbuscula S arctica S atrocinerea S aurita S bicolor S breviserrata S burjati
35. ressaceae Juniperus Juniperus communis 3 Pinus Cembra 2 Abies Alba Taxus 1 Cedrus Pinus halepensis Pinus pinaster c1 Orge d hiver c2 Orge de printemps c3 Froment d hiver c4 Froment de printemps c5 Pommes de terre c6 Betterave c7 Colza c8 Mais d ensilage c9 Faba bean There are 9 plant parameters input files that contains several plant parameters that are comprehensively detailed below File Parameter name Description Units bagibm dat alvsw Short wave albedo alvlw Long wave albedo rdveg Root depth of the vegetation mm t1 Temperature for beginning of LAI increase C t2 Temperature for end of LAI increase C xlmin Minimal LAI value before t1 xlmax Maximal LAI value before t2 z0vw Roughness length in winter zOvs Roughness length in summer m CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 11 disd Displacement height zzra Reference height for wind measurements m emv Emissivity of vegetation cover bagpar dat g0 intercept for the stomatal conductance pumol m s gl slope for the stomatal conductance splai specific leaf area m gC delc2 Fractionation linked to diffusion through stomatal cavities for each species xi 1 Parameter of the equation for carbon allocation to pool gC m xi 2 Parameter of the equation for carbon allocation to pool gC m resef Parameter of the equation for available biomass for bud xk rootf Fraction of the assimilates that are allocated to the roots b
36. seudomillefoliatus R pseudomontanus psilostachys R puberulus R pygmaeus pyrenaeus R radinotrichus R repens reptans R revelieri R rionii R rumelicus sardous R sartorianus R sceleratus seguieri R serbicus R silanus silvisteppaceus R sphaerospermus spicatus R sprunerianus R stojanovii strigulosus R subhomophyllus sulphureus R thasius R thora thracicus R traunfellneri R trichophyllus trilobus R tripartitus R velutinus venetus R villosus R wettsteinii weyleri Stellaria bungeana S calycantha S crassifolia S crassipes S cupaniana S fennica S graminea S hebecalyx S holostea S humifusa S longifolia S longipes S media S neglecta S nemorum S pallida S palustris S uliginosa Thalictrum alpinum T aquilegiifolium T calabricum T flavum T foetidum T lucidum T macrocarpum T minus T morisonii T orientale T simplex T speciosissimum T tuberosum T uncinatum VADNADNADAAAAAAAAAAAAAAAAANA Renoncules Stellaires Pigamon 68 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Achillea Achillea millefolium A ptarmica Achill es Alchemilla Alchemilla alpina A glabra A glaucescens Alch milles A glomerulens A gracilis A monticola A murbeckiana A plicata A propinqua A sarmatica A subcrenata A vestita Angelica Angelica archangelica A sylvestris Ang liques
37. sfer within the canopy Used in npp cal Used in drainage Random estimation for temperatures Arranges variables at different time steps Determines the maximum lai when soil water is missing Writes first year results Writes results to results files Integrates variables over the year Used in zonepxl2 Determines the geoclimatic zone corresponding to the studied region SEPTEMBER 2013 18 4 Technical issues 4 1 Compilation and run CARAIDB is written in FORTRAN and needs a FORTRAN compiler to be used The freeware INTEL Fortran Compiler can be recommended Using this software the code is compiled using the following command on UNIX systems ifort caraib f Then the model is run by typing in the command line a out The FORTRAN compiler can be installed on your own PC Alternatively you can use a remote desktop dedicated to computation with CARAIB 5 List of abbreviations e BAG Bioclimatic Affinity Group e CARAIB CARbon Assimilation In the Biosphere e GPP Gross Primary Productivity e IBM Improved Bucket Model e LAI Leaf Area Index e NPP Net Primary Productivity e PFT Plant Functional Types 6 List of References e Dury M A Hambuckers P Warnant A Henrot E Favre M Ouberdous L Francois Responses of European forest ecosystems to 21st century climate assessing changes in interannual variability and fire intensity iForest Biogeosciences and Forestry 4 82 89 2011 e Francois L Delire C
38. ssubico auricomus cassubicus R caucasicus R chius circinatus R clethraphilus R concinnatus cordiger R cornutus R cortusifolius crenatus R creticus R crimaeus cupreus R cymbalaria cymbalariifolius R degenii R demissus dissectus R fallax R ficaria ficarioides R flabellifolius R flammula fluitans R fontanus R glacialis gmelinii R gouanii R gracilis gramineus R granatensis R gregarius grenieranus R hayekii R hederaceus henriquesii R hungaricus R hybridus hyperboreus R illyricus incomparabilis R isthmicus R kalinensis kamchaticus R lanuginosus lapponicus R lateriflorus R lingua longipes R macrophyllus R magellensis malessanus R marginatus marschlinsii R marsicus R megacarpus miliarakesii R millefoliatus R millii monophyllus R monspeliacus montanus R montanus R muricatus Renou es Renonculac es Renoncules 67 Annexe 1 1 BAG Taxons palynologiques Taxons botaniques Noms vernaculaires 24 Ranunculus Stellaria Thalictrum nigrescens R nivalis R nodiflorus odessanus R olissiponesis R ololeucos omiophyllus R ophioglossifolius oreophilus R oxyspermus R pallasii paludosus R pannonicus parnassiifolius R parviflorus pedatus R peltatus R penicillatus platanifolius R platyspermus pollinensis R polyanthemos polyphyllus R polyrhizos R pratensis p
39. st start in column 26 002 2002 003 2003 SEPTEMBER 2013 380 380 380 380 380 380 ON U1 HW A AAA A EH 2004 2004 2005 2005 2006 2006 2007 2007 2008 2008 2009 2009 a Inputs parameters The first lines of the configuration file contain general parameters that mainly serve to define the type of the simulation Parameter name Description isteady ny0max 1 to call generator ifrac ifrac_rd ilai_rd idayt ifull ifire iprt fire nyrmax stept nyrprt nstprt iread iczon idaily in idaily ou pixel numb 1 for transient run will simulate nyOmax times the same year before the first year of simulation as a warm up of the model 0 for steady state run Number of year iterations between water and carbon modules if isteady 1 This time delay expressed in years is used to allow the model to reach the equilibrium warm up of the model Must be set to 1 to call weather generator not needed with daily climatic inputs 1 if you want to calculate fraction of the pixel covered by each BAG 0 for fixed fractions ifrac rd must be set to 1 with ifrac 0 1 if you read the fraction of the pixel covered by each BAG to initialise the run 1 if you want to read min and max LAI to initialise hydrological module 1 to include diurnal cycle in the hydrological cycle 2 otherwise 1 to write daily results of IBM will generate huge amounts of outputs so it is recommended to av
40. svey Sum of interception of rainfall mm eiry Sum of gC m gC m gC day gC m mm sim W m mm mm mm mm mm 2 C C mm or snow evaporation mm sney Sum of potential m m for evaporation mm pety wbudy wbudy Minimal soil water soil water content m3 m aswmin fractional vegetation cover fveg Yearly minimal and maximal values of LAI per BAG Minimal values are written first for each BAG then maximal values Monthly or daily values of the sensible heat flux Monthly or daily values of the latent heat flux content m m W m W m CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 3 4 Description of the code The CARAIB model is coded in a unique FORTRAN file that is usually called caraib f This file is described in this section 3 4 1 Pseudocode Below is a brief description of the code of the CARAIB model namely the pseudocode This pseudocode is not exhaustive but presents all the important steps of the model The names of the subroutines are shown in italic Read caraib dat input file open input5 Call routines for computing some constants LOOP over years Read time dependent input files open file IF stated call the weather generator generator ELSE read weather data ENDIF IF it is the first year Read time independent input files read eco Read initial conditions files read init Determine the climate zone for all pixels ENDIF LOOP over pi
41. t filenameYEAR res with YEAR being the year File File number Parameter name Description Units aburn res 75 Burned area Monthly or daily burned area m aet res 33 Actual evapotranspiration Monthly or daily values of actual evapotranspiration mm Monthly or daily values of the average albedo of the alb res 39 Albedo pixel Amount of carbon stocked in the following pools Total Carbon Leaf Carbon Structural Carbon i e Csoil res 67 Amount of carbon in trunks Soil Carbon gC Cveg res 66 Amount of carbon Amount of carbon stocked per BAG gC drn res 36 Drainage Monthly or daily values of drainage mm emisf res 52 Surface emissivity Monthly or daily values of the surface emissivity fburn res 74 Burned pixel fraction Monthly or daily burned pixel fraction Monthly or daily values of the snow free green cover Jos res 43 Snow free green cover fraction Downward infrared Monthly or daily values of the downward infrared fird res 45 radiation radiation Wim frac res 60 Fraction of each BAG frcC13 res 68 Isotopic fraction of C13 Isotopic fraction of C13 per BAG fsn res 35 Fraction of snow Monthly or daily values of fraction of snow Monthly or daily values of the incoming solar fsol res 48 Incoming solar radiation radiation W m Yearly cumulated degree days gddO and gdd5 are presented GddO is the sum of degrees days above gdd res 72 Cumulated degree days 0 C Gdd5 is the sum of degrees days above 5 C C da
42. tia Athamanta Bunium Bupleurum Carum Chaerophyllum Conopodium Daucus Echinophora Eryngium Falcaria Ferula Foeniculum Heracleum Laserpitium Meum Myrrhis Oenanthe Pastinaca Peucedanum Pimpinella Ptychotis Sanicula Scandix Selinum Sesli Silaus Smyrnium Torilis Trinia Trochischanthes ou Tubuliflores Cichorioid es ou Liguliflores Gramin es Myriophylle Ombellif res 63 Annexe 1 1 BAG Taxons Taxons botaniques Noms vernaculaires palynologiques Anthemis Anthemis arvensis A cotula A tinctoria Anth mis Artemisia Artemisia absinthium A campestris Armoises A vulgaris Bidens Bidens cernua B tripartis B radiata Bidens Brassica Brassica balearica B barrelieri B bivoniana Choux moutarde 23 Calystegia sepium Carduus Euphorbia Hypericum Knautia arvensis Lamium Lysimachia Lythrum Papaveraceae Plantago P major Polygala Potentilla Sedum Stachys cadmea B cretica B drepanensis elongata B fructicosa B glabrescens gravinae B incana B insularis B juncea macrocarpa B montana B nigra nivalis B oleracea B oxyrhina procumbens B rapa B repanda rupestris B souliei B tinei B tournefortii villosa Calystegia sepium Carduus aca C crispus C nutans Euphorbia cyparissias E esula E exigua E helioscopia E palustris Hypericum hirsutum H humifusum H maculatum H montanum H perforatum H pu
43. tran code of the CARAIB model e caraib out compiled version of caraib f e caraib dat configuration file with list of inputs and input and output files CARAIB USER s GUIDE 1 0 SEPTEMBER 2013 4 e clim directory containing climatic input files e common directory containing all commons used by CARAIB e gene directory containing the weather stochastic generator e plantparam directory containing plant parameters files for the BAGs e results directory containing all output files These files are comprehensively described in the sections hereafter 3 2 Description of input files 3 2 1 The configuration file caraib dat CARAIB works with a configuration file in which all input parameters and paths to input files are set It is the most important file for CARAIB users CARAIB reads in this file the specific parameters for each run If you change the name of this file pay attention to change it in the main code around line 374 in caraib f or search after dat in caraib f This file looks like that isteady nyOmax 200 1 to call generator ifrac 1 calc frac ifrac_rd ilai_rd idayt ifull ifire nyrmax stept nyrprt nstprt iread iczon idaily in idaily ou pixel number 20 resolution lg lat 0 02778 exc obl xlsper 0 016724 23 447 282 16 nher nbush ntree nc 5 7 13 9 fil ext inp weather dat fil ext results res soil texture clin eco dat air temp climatol clim tem dat precip climatol clim
44. type Path for the monthly or daily temperatures for the studied year climate for steady state run C This path refers to a set of files with one file per year following the format temYEAR dat with YEAR being the year e g tem2012 dat This remark applies to the next 7 files Path for the monthly or daily values of diurnal variation of the temperature daily difference between maximal and minimal temperatures for the studied year C Path for the monthly or daily values of precipitations for the studied year mm month Path for the monthly or daily values of percentage of sunshine hours 96 Path for the monthly or daily values of air relative humidity for the studied year 96 Path for the monthly or daily values of wind speed at the surface for the studied year m s Path for the monthly or daily values of lightning flash frequency for the studied year number of flashes per km2 per month Used in the fire module only Path for the values of the fraction of the land use classes for each pixel Path for the directory containing the weather stochastic generator gene Path for the parameter file used by hydrological module IBM bagibm dat Path for the parameter file of climatic limits for BAG presence bagtol dat Path for the parameter file of carbon module parameters bagpar dat Path for the parameter file of age classes parameters claspar dat Path for the parameter file of C N of metabolic leaves and structur
45. ulvaria Aethionema Allaria Alyssoides Alyssum Andrezeiowskia Arabidopsis Arabis Armoracia Aubretia Aurinia Barbarea Berteroa Biscutella Bivonea Boleum Boreava Bornmuellera Brassica Braya Bunias Cakile Calepinia Camelina Capsella Cardamine Cardaminopsis Cardaria Carrichtera Chorispora Chrysochamela Clausia clypeola Cochlearia Coincya Conringia Coronopus Crambe Degenia Degenia Descurainia Didesmus Diplotaxis Diptychocarpus Draba Drabopsis Enarthrocarpus Eremoblastus Erophila Eruca Erucaria Erucastrum Erysimum Eucidium Eutrema Euzomodendron Fibigia Goldbachia Guiraoa Hesperis Hirschfeldia Hornungia Hugueninia Hymenolobus Iberis Isatis Jonopsidium Kernera Laevenworthia Lepidium Leptaleum Litwinowia Lobularia Lunaria Lycocarpus Malcolmia Maresia Matthiola Megacarpaea Moricandia Morisia Murbeckiella Myagrum Neotorularia Neslia Notoceras Pachyphragma Parrya Peltaria Petrocallis Pritzelago Raphanus Rapistrum Rhizobotrya Ricotia Rorippa Schivereckia Sinapis Sisymbrella Sisymbrium Sobolewskia Sterigmostemmum Subularia Succowia Tauscheria Teesdalia Teesdaliopsis Tetracme Thellungiella Thlaspi Vella Athraphaxis Calligonum Emex Fallopia Koeningia Oxyria Polygonum Reynoutria Rheum Rumex Ch nopode Ans rine Crucif res Polygonac es 66 Annexe 1 1 BAG Taxons palynologiques Taxons botaniques Noms ver
46. xels Read climatic vegetation and soil data read in Read crops cover fractions read cult Determine the climate zone for the pixel Estimate daily climatic conditions daily weather Calculates solar fluxes and related parameters solar Set vegetation fraction set frac Calculates drainage drainage Set initial conditions for some hydrological variables init c Set PFT establishment oft estab Calculate the external conditions i e air temperature air relative humidity irradiance and aerodynamic and boundary resistance at an hourly time step cal in Initialisation of some variables ponc init Set carbon pool values set cpools Initialisation of the LAI limitation due to water stress lailim init Calculate the NPP npp cal Run the fire module fire Calculate the mortality mortality Calculates the correction linked to the fire module correction Calculates the soil respiration soil resp Calculates the vegetation succession i e the vegetation dynamics new frac Gather pixel results record grid ENDDO Write results wri 1st ENDDO CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 16 3 4 2 Frequently used variables e ny0 is the counter of the number of years up to nyrmax the total number of years e ngtis the counter of the number of pixels up to n pix the total number of pixels e ip is the counter of the number of PFT up to npft0 the total number of PFT e idn is the day number e steptis the integration step
47. y Gross Primary gpp res 65 Productivity Annual sum of GPP per BAG gC m Gross Primary gppmth res 56 Productivity Monthly or daily values of the GPP gC m Monthly or daily values of the heat flux to the grf res 41 Ground flux ground Wim lai res 44 Leaf area index Monthly or daily values of the leaf area index m m laimoy res 69 LAI per BAG Yearly average of LAI per BAG m m laimth res 59 Leaf area index Monthly or daily values of the leaf area index m m CARAIB USER S GUIDE 1 0 SEPTEMBER 2013 14 nepmth res npp res nppd res nppmth res pet res pfire res rbl res Rmin res rn res run res sf res sml res sne res Sve res sw res Tdmin res Tmmin res ts res water yr res x lai min max res xh res xle res 38 63 40 34 51 50 37 31 70 71 42 64 46 47 Net Ecosystem Productivity Net Primary Productivity NPP per day Net Primary Productivity Potential evapotranspiration Probability of fire aerodynamic resistance for water Ratio of LAImax Net radiation Runoff Snow fall Snow melt Snow evaporation LAlmin Soil vegetation evapotranspiration Soil water Min and max temperature Min and max monthly temperature daily Temperature of the surface Yearly water budget Min and max LAI Sensible heat flux Latent heat flux Monthly or daily values of the NEP Annual sum of NPP per BAG Daily values of NPP per BAG Monthly or daily values of the NP
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