Refactoring v4.1 & v4.2

[sylvainschmitt]

• crown.cpp > to be removed in 4.1
• input.cpp
  • BuildSpeciesRegistry
  • AssignSpeciesParam
  • AssignValuePointCloud
  • ReadInputGeneral
  • ReadInputSpecies
  • ReadInputDailyVar
  • ReadInputClimate
  • ReadInputSoil
• lookup-table.cpp
  • InitialiseIntraspecific
  • InitialiseLookUpLAImax
  • InitialiseLookUpTables
• memory.cpp
  • InitialiseOutputStreams
  • Initialise
  • InitialiseABC
  • ReadInputPointCloud
  • AllocMem
  • FreeMem
• output.cpp (maybe to split in 4.2 or 4.3)
  • Average
  • OutputField
  • OutputSnapshot
  • OutputVisual
  • OutputCHM
  • OutputLAI
  • MakeCHMSpikefree
  • GenerateVoxelreturnsALS
  • TrackingData_andOutput
  • CloseOutputs
  • Tree::StartTracking
  • Tree::OutputTreeStandard
  • Tree::histdbh
  • Tree::Average
  • OutputABC
  • OutputABCWriteHead
  • OutputABCconserv...
  • OutputABC_ground
  • OutputABC_species
  • OutputABC_CHM
  • UpdateMovingAverageABC
  • UpdateDBHtrackingABC
  • UpdateTransmittanceCHMABC
• simulation.cpp
  • Evolution
  • GetTimeofyear
• species.cpp
  • Species
  • Init
• tree.cpp in 4.1 with everything below and in 3 files in 4.2
  • demography.cpp (only in 4.2)
    • Tree
    • Update
    • Birth
    • BirthFromInventory
    • InitialiseLeafPools
    • RecruitTree
    • TriggerTreefall
    • TriggerTreefallSecondary
    • Treefall
    • Death
    • DeathRate
    • DeathRateNDD
  • assimilation.cpp (only in 4.2)
    • Fluxh
    • Water_availability
    • Water_uptake
    • GPPleaf
    • dailyGPPleaf
    • dailyGPPcrown
    • Rdayleaf
    • dailyRdayleaf
    • FluxesLeaf
    • dailyFluxesLeaf
    • CalcJmaxm
    • CalcVcmxm
    • CalcRdark (à convertir en méthode ?)
  • allocation.cpp (only in 4.2)
    • Growth
    • CalcLaimax
    • UpdateLeafDynamics
    • UpdateTreeBiometry
    • UpdateVolumeDensity
    • CalcAGB
    • CalcIncrementDBH
    • CalcCarbonStorageMax
    • CalcCt
    • CalcLeafLifespan
    • predLeafLifespanKikuzawa
    • UpdateHieght
    • UpdateCR
    • UpdateCD
    • GetRadiusSlope
    • GetRadiusCylinder
    • GetCrownIntarea
    • DetDensityGradient
    • GetDensityUniform
    • CalcHeightBaseline
    • CalcCRBaseline
    • CalcCDBaseline
    • KeepFloatAsIs
    • KeepIntAsIs
    • Quad
• field.cpp > new to 4.1 or a rename of crown.cpp, and MIP_ probably to be removed
  • UpdateSeeds
  • UpdateField
  • FillSeed
  • DisperSeed
  • CalcLAI
  • CalcIntabsorb
  • GetPPFDAbove
  • GetCanopyEnv
  • AddCrownVolumeLayer
  • GetCrownAreaFilled
  • LAI2dens_cum
  • LAI2dens
  • UpdateLAI3D
  • UpdateCHMvector
  • UpdateCHM
  • MPI_ShareSeed
  • MPI_ShareField
  • MPI_ShareTreefall
• troll.cpp
  • main
• internal/lookup-tables_cache.cpp
  • SaveLookUpTablesToCache
  • LoadLookUpTablesFromCache
• internal/param_registry.cpp
  • SetParameter
  • RegisterParameters
  • AssignParamFromRegistry