First commit with the code Hector shared with me

PYR00_R2_ssp245.setup

@@ -0,0 +1,250 @@
+# Forceps setup file
+
+siteFileName = 01_SITE/forceps.PYR00.site
+
+speciesFileName = forceps3.New_species
+
+defaultClimateFileName = 02_CLIMATE/Climate/PROJECTIONS/MPI-ESM1-2-HR/ssp245/forceps.MPI-ESM1-2-HRssp245PYR00.climate
+defaultClimateIsDaily = true
+
+initDate = 2022
+randomSeed = 123
+
+inventory = true
+inventoryFileName = 03_INVENTORY/forceps.PYR00.inv
+
+bareGround = false
+bareGroundPatchN = 1
+bareGroundPatchArea = 100
+
+equilibriumInitialCanopy = true
+# equilibriumInitialCanopy = false
+
+sureauSoilParametersFileName = 04_SOIL/SurEauSoilParameters_PYR00.txt
+
+management = true
+managementFileName = 05_MANAGEMENT/forceps.PYR00_R2.management
+
+potentialSpeciesList = 0 13 15 17 18 20 21 23 25 31
+
+phenofitActivated = true
+phenofitPath = 06_PHENOLOGY/PYR00/
+phenofitSpeciesCorrespondanceFileName = phenofit4/phenofitSpeciesCorrespondance.txt
+
+####
+
+adaptiveMode = false
+adaptiveInputCompleteExport = inputCompleteExport.adaptive
+# adaptiveVarianceLevel: ADAPTIVE_VARIANCE_LEVEL_LOW, ADAPTIVE_VARIANCE_LEVEL_MEDIUM or ADAPTIVE_VARIANCE_LEVEL_HIGH
+adaptiveVarianceLevel = ADAPTIVE_VARIANCE_LEVEL_LOW
+# adaptiveTradeOffOption: ADAPTIVE_NO_TRADEOFF_OPTION, ADAPTIVE_TRADEOFF_DRTOL_OPTION or ADAPTIVE_TRADEOFF_G_OPTION
+adaptiveTradeOffOption = ADAPTIVE_TRADEOFF_G_OPTION
+adaptiveInventoryPatchN = 50
+adaptiveInventoryPatchArea = 800
+
+adaptiveInitial_laSd = 0
+adaptiveInitial_drtolSd = 0
+adaptiveInitial_gSd = 0
+#adaptiveInitial_laSd = 0.03
+#adaptiveInitial_drtolSd = 0.1
+#adaptiveInitial_gSd = 5
+
+adaptiveExtraVariance_drtol = 0.03
+adaptiveExtraVariance_g = 5
+
+# fc+ld-8.11.2022
+adaptiveConstantVarianceMode = false
+adaptiveConstantVariance_laSd = 0.8
+adaptiveConstantVariance_gSd = 32
+adaptiveConstantVariance_drtolSd = 0.03
+
+adaptiveMultiNormalCorrelation_g_la = 0
+adaptiveMultiNormalCorrelation_drtol_g = -0.5
+adaptiveMultiNormalCorrelation_la_drtol = 0
+
+adaptiveTreeReproductionWeight = true
+
+adaptiveReadSpeciesParametersInCompleteExport = false
+
+################### adaptive2 ###################
+
+# User must choose adaptiveMode or adaptive2Mode but not both
+
+adaptive2Mode = false
+adaptive2FileName = forcepsAdaptive2.trait
+
+#####################################################
+
+# fc+ld-4.1.2023
+adaptiveHeritability = 0.3
+regenerationForclimLike_withMigration = false
+# ld-3.7.2023 Added a migration multiplicator to control the number of migrant per patch each year
+migrationFactor = 1
+
+#distProba = 0.5
+distProba = 0.005
+#distProba = 0
+
+#deathProbaCoef = 0
+deathProbaCoef = 4.605
+
+#slowGrowthProba = 0
+slowGrowthProba = 0.368
+
+slowGrowthTime = 2
+
+# If true, trees get a real crown length
+crownLengthOption = true
+crownLengthImpactOnGrowth = true
+
+# Regeneration: one option out of these 3 must be selected
+
+regenerationMaxTreesPerPatchOption = false
+regenerationMaxTreesPerPatchNumber = 50
+regenerationMaxTreesPerPatchWithNTries = false
+regenerationMaxTreesPerPatchNTries = 5
+
+regenerationSeedlingsPerPatchOption = false
+regenerationSeedlingsPerPatchNumber = 100
+
+regenerationForclimLike = true
+
+
+regelibActivated = false
+regelibFileName = 
+
+
+# Regeneration: additional options
+
+regenerationActualSpeciesOnly = false
+regenerationActualSpeciesOnlyAtPatchLevel = false
+regenerationConstraint = true
+# fc+xm+lv-10.5.2021 added regenerationActualSpeciesOnlyAbundance
+regenerationActualSpeciesOnlyAbundance = false
+# fc+ld-24.2.2023 addedregenerationSpeciesContributionsBasedAbundance
+regenerationSpeciesContributionsBasedAbundance = false
+
+establishmentProbabilityCoef = 0.1
+establishmentProbabilityCoef = 0.1
+
+ppMothActivated = false 
+ppMothRegionalPercentageOfInfestedTreesOption = false
+ppMothRegionalPercentageOfInfestedTrees = 0.12
+
+variability = false
+variabilityFileName = forceps.fitnessVariability
+
+climaticFitness = false
+fitnessImpactsGrowth = false
+
+#droughtStressOption = FORCLIM_LIKE_DROUGHT_STRESS
+droughtStressOption = PATCH_LEVEL_DROUGHT_STRESS
+
+#trunkVolumeOption = FORCLIM_TRUNK_VOLUME
+trunkVolumeOption = EMERGE_TRUNK_VOLUME
+
+leafLossImpactOnGrowthFactor = 0.5
+frostLeafLossImpactOnLAI = true
+
+reproductiveSuccessImpactOnRege = true
+
+
+# Extra options
+canopyLayerThickness = 1
+
+crownA1ReversionFactor = 0.05
+
+variableAllometry = true
+
+treeHeightFromInventory = true
+
+conicalCanopyShadows = true
+
+equilibriumError = 0.05
+
+layeredCrownAndHeightPlasticityCalculation = true
+
+speciesCrownShapeParameters = true
+
+speciesSpecificLeafArea = true
+
+densityDependentLightAttenuation = true
+
+leafPhenologyImpactOnLightCompetition = true
+leafPhenologyImpactOnLightCompetition_GDDweights = false
+
+percentOfRainExclusion = 0
+
+
+# deadWoodModule
+deadWoodActivated = true
+initialLitterBiomassInformation = initialLitterBiomass()
+#initialLitterBiomassInformation = initialLitterBiomass(Phal(2000000,5))
+#initialLitterBiomassInformation = initialLitterBiomass(kSName_1(Biomass_kg_ha,mean_diameter_cm);kSName_2(Biomass_kg_ha,mean_diameter_cm))
+
+yassoActivated = true
+yassoParametersFileName = yassoParameters.txt
+yassoSpeciesFileName = YassoSpeciesParameters.csv
+
+soilCarbonEquilibriumInitialization = false
+soilCarbonInitializationInformation = soilCarbonInitializationInformation(5000;1970;2020;2;0;0)
+#soilCarbonInitializationInformation = soilCarbonInitializationInformation(calibrationYearLength;climateStartYear;climateEndYear;yearlyMortalityPercentRate;yearlyCutPercentRate;extractedBranchPercentage)
+
+canopyStructureMemory = true
+microClimateActivated = true
+
+activateTREMCalculator = true
+
+
+# Options for Sureau linking
+
+sureauActivated = true
+
+sureauExplicitScheme = false
+
+sureauSmallTimeStep = 1200
+
+sureauTimeStep = 1
+
+sureauClassNbPerSpecies = 10
+
+sureauMortalityModule = true
+
+sureauGrowthModule = true
+
+
+# WRITING_DISABLED, WRITING_FREQUENCY_YEAR, WRITING_FREQUENCY_DAY, or a number of seconds
+sureauWritingFrequency = WRITING_FREQUENCY_DAY
+
+yearToYearPLC = true
+
+growthToCavitationRepairConversionFactor = 1
+
+droughtInducedDefoliation = true
+
+droughtInducedDefoliationImpactOnGrowth = true 
+
+droughtInducedDefoliationImpactOnLightCompetition = true
+
+explicitRootLength = true
+rootLengthPlasticity = true
+
+cavitationMortalityTresholdPercentage = 20
+
+# Can be set either to a number of years > 1 or to -1. In wase -1 is used, no delay is involved and mortality from PLC is evaluated each year
+plcMortalityDelayYear = -1
+
+# If true, must be used with plcMortalityDelayYear = 1 is false, plcMortalityDelayYear must be a different int than 1
+resetPLCAfterMortalityTest = false 
+
+sureau_drtolFromSMRI = false
+
+# LAI_BASED_TRUNK_INTERFACE_AREA_OPTION, AGGREGATE_TRUNK_INTERFACE_AREA_OPTION, SUMMED_TRUNK_INTERFACE_AREA_OPTION
+
+sureauTrunkInterfaceAreaOption = LAI_BASED_TRUNK_INTERFACE_AREA_OPTION
+
+# SPECIFIC_TO_TREE_TYPE, GROWTH_BASED_ONLY (original method implemented by Tanguy) or SPECIFIC_TO_TREE_TYPE_GROWTH_DEPENDENT (mix of both methods)
+cavitationReparationMethod = GROWTH_BASED_ONLY
+
+rootDepthEquilibriumCalibration = false
+rootDepthInitializationInformation = rootDepthInitializationInformation()