Changes between Version 14 and Version 15 of Documentation/TrunkFunctionality4


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Timestamp:
2020-03-09T14:15:40+01:00 (4 years ago)
Author:
luyssaert
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  • Documentation/TrunkFunctionality4

    v14 v15  
    9696Previously there was a functional link between C and N-allocation and the hydraulic architecture of a plant because both approaches used the same parameter k_root. In ORCHIDEE-CAN k_root described the conductivity of the fine roots and the soil. In ORCHIDEE trunk 4 this joined conductivity has been split in a fine root conductivity and a soil to root conductivity. Allocation should make use of both conductivities but soil to root conductivity cannot be easily calculated when needed in the allocation. This is subject to future developments. Accounting for the soil to root conductivity in the allocation would imply an adaptation of plant growth to its environment.   
    9797 
     98 
    9899=== Anthropogenic species change (r6614) === 
    99100Following a disturbance (which could be a clear cut), tree species changes and forest management change can be prescribed or read from a map in ORCHIDEE trunk 4. Set '''ok_change_species''' = y, '''read_species_change_map''' = y, and '''read_desired_fm_map''' = y and specify the paths of those maps in the COMP/stomate.card. A example of such a configuration can be found in config/ORCHIDEE_OL/OOL_SEC_STO_FG5. This functionality replaces the DGVM in areas where humans rather than nature govern species distribution, for example, Europe. Note that there are some constraints on the possible species changes. If the forest is unmanaged (fm=1), the code assumes that nature will determine the species rather than humans. Anthropogenic species change has not been developed to work together with land cover change. For the moment it is one or the other. When testing this functionality read_species_change_map and/or read_desired_fm_map could be set to n. The new forest management strategy can then be simply prescribed by setting the parameter '''fm_change_force''' to one of the four fm strategies. Likewise the new species can be prescribed by setting the parameter '''species_change_force''' to the desired PFT number. 
    100101 
     102 
    101103=== Bare soil (r6614) === 
    102104The flag '''ok_bare_soil_new''' controls how the bare soil is perceived and calculated. If set to FALSE the total bare soil is still calculated as a function of veget. When a deciduous PFT sheds its leaves, the gaps in the forest will contribute to bare soil fraction in the grid. Although this approach was introduced a long time ago to get acceptable evaporation estimates from forest, the approach also resulted in using the albedo of deserts as the background albedo of forest gaps. The new albedo scheme (see Albedo and Background albedo) considers a specific background albedo for each PFT and calculates the albedo of the PFT including the canopy gaps. Moving gaps to the bare soil is no longer needed. So, if '''ok_bare_soil_new''' is set to TRUE, canopy gaps no longer contribute to the bare soil. It needs to be tested what will happen with the evaporation in the single-layer model. The multi-layer energy budget should be able to correctly deal with the gaps in the canopy because the diffusivity will increase when the canopy is becoming sparser. 
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    104106At present the default settings combine the new albedo scheme with the single layer energy budget (enerbil) and '''ok_bare_soil_new''' = n. The consequences of this combination of settings should be evaluated against observations. 
    105107 
     108 
    106109=== Bark beetles (r6614) === 
    107110The bark beetle module was developed such that it interacts with the windthrow module. If you want to activate it use the flag OK_PEST=y in the run.def. To specify which PFT may be affected by bark beetles use BEETLE_PFT_xxx= TRUE where XXX is the pft you interested in. Note that for the moment bark beetles in ORCHIDEE is parameterized only to work with Picea abies. 
    108111 
     112 
    109113=== C13 (r6614) === 
    110114The concentration of C13 in the leaves can be calculated by setting '''ok_c13''' to y in the run.def. This calculation follows Farquhar's approach and is currently limited to the fractionation in the leaves. Following changes to the recalculation of GPP under plant water stress the calculation of Ci is no longer accurate. This may have broken the functionality to calculate C13. Needs to be tested. 
     115 
    111116 
    112117=== Configurations (r6614) === 
    … …  
    124129* FORCESOIL: was restored for ORCHIDEE trun 3 but was not maintained for ORCHIDEE trunk 4 (see ticket #684). 
    125130 
     131 
    126132=== Consistency checks (r6614) === 
    127133The code distinguishes between three options to check for mass and surface conservation. These options are controlled by the parameter '''err_act'''. Always use err_act = 3 when developing and testing the code. Note that in addition to checking for mass balance closure ORCHIDEE trunk 4 will also check for the conservation of veget_max and frac_nobio. This is useful to make sure no surface area is lost when moving biomass from one PFT to another following natural disturbances, forest management, land cover changes and when using age classes. In some parts of the code, for example, modules that deal with disturbances, it is assumed that the tallest trees are stored in the last diameter class. When the difference in diameter between diameter classes becomes very small, this assumption could be violated. Therefore, the diameter classes are sorted to enforce the assumed order and where needed the order is checked. 
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    139145 
    140146 
    141 ++++ CONTINUE CHECKING +++++ 
    142 === Diameter classes (CHECK) === 
     147=== Diameter classes (r6614) === 
    143148Diameter classes were introduced to better simulate the canopy structure, they are a tool to simulate heterogeneity within a single PFT. Given that the canopy is the interface between the land and the atmosphere this feature has effects well beyond forest management. Stand structure was observed to affect albedo, transpiration, photosynthesis, soil temperature, roughness length, and recruitment. Using diameter classes adds very little complexity to setting-up the simulations as well as to the output files. The complexity is mostly within the code.  
    144149 
    145 The computational cost of using diameter classes is negligible and when a reasonable low number of diameter classes is used, the memory cost remains very small as the dimensions of only two variables are increased. The number of diameter classes is the same for all PFTs and is set by the parameter '''NCIRC'''. ORCHIDEE-CN, and ORCHIDEE-CNP are coded and used for NCIRC = 1. ORCHIDEE-CAN and ORCHIDEE-CN-CAN are coded and tested for NCIRC = 3 but the model has been run with one diameter class as well +++REDO. Until further testing, three diameter classes are considered sufficient. 
    146  
    147 Given earlier choices in ORCHIDEE, we either need to define the boundaries of each diameter class or the diameter distribution. While developing the code, we considered the second approach the most flexible. To allow maximal flexibility, each diameter class needs to be defined separately by the variable '''CIRC_CLASS_DIST_0000X''', where X is the number of the diameter class. The smallest number presents the smallest diameter class. From literature it is known that a truncated exponential distribution is a good first guess: 
     150The computational cost of using diameter classes is negligible and when a reasonable low number of diameter classes is used, the memory cost remains very small as the dimensions of only two variables are increased. The number of diameter classes is the same for all PFTs and is set by the parameter '''NCIRC'''. ORCHIDEE-CN, and ORCHIDEE-CNP are coded and used for NCIRC = 1. ORCHIDEE trunk 4 was coded and tested for NCIRC = 3. Until further testing, three diameter classes are considered sufficient although for some specific application, i.e., simulating tree ring width NCIRC = 5 resulted in slightly better model performance. The branch ORCHIDEE-CN-CAN that preceded this trunk version has been run with one diameter class as well (this should be confirmed for ORCHIDEE trunk 4).  
     151 
     152Given earlier choices in the ORCHIDEE model, we either need to define the boundaries of each diameter class or the diameter distribution. While developing the code, we considered the second approach the most flexible. To allow maximal flexibility, each diameter class needs to be defined separately by the variable '''CIRC_CLASS_DIST_0000X''', where X is the number of the diameter class. The smallest number presents the smallest diameter class. From literature it is known that a truncated exponential distribution is a good first guess: 
    148153{{{  
    149154CIRC_CLASS_DIST_00001=9 
    … …  
    153158The above declaration implies that 9/15th of the trees will always be in the smallest diameter class, 5/15th will be in the medium class and 1 tree out of 15 will be in the largest diameter class. These ratios are kept throughout the simulations and the boundaries of the diameter classes are adjusted to respect this constraint. Consequently, an even-aged stand will be simulated with three diameter classes where the diameter of the first class may be, for example, 20.3 cm, the diameter of the second class 20.4 cm and the diameter of the third class 20.5 cm. The same code and set-up allows to simulate, in the same simulation, an uneven-aged stand for the same PFT but in a different pixel with, for example, the smallest diameter 7 cm, the medium diameter 25 cm and the largest diameter 45 cm. 
    154159 
     160 
    155161=== Forced clear cut (r6614) === 
    156 '''OK_CLEARCUT''' is a flag used to force ORCHIDEE-CN-CAN to clearcut a forest after one year of simulation. This flag is set to TRUE in order to start a new stand at the beginning of the FIN step in ENSEMBLE runs. It helps us to control the stand age at the end of the HIST step. If you want to use this flag for other purposes, do not forget that a clearcut means that the majority of the living biomass is removed (circ_class_biomass for sapwood and heartwood), but the other pools are transferred in the litter pool (leaf, branches, fruit, fine root). Note that if '''OK_CLEARCUT''' is used, the model will clearcut at the end of every year. The typical set-up should be: 300 years of spin-up with '''OK_CLEARCUT''' set to FALSE, 1 year with '''OK_CLEARCUT''' set to TRUE, a simulation with the length similar to the age of the forest with '''OK_CLEARCUT''' set to FALSE.  
     162'''OK_CLEARCUT''' is a flag used to force ORCHIDEE trunk 4 to clearcut a forest after one year of simulation. This flag is set to TRUE in order to start a new stand at the beginning of the FIN step in ENSEMBLE runs. It helps us to control the stand age at the end of the HIST step. If you want to use this flag for other purposes, do not forget that a clearcut means that the majority of the living biomass is removed (circ_class_biomass for sapwood and heartwood), but the other pools are transferred in the litter pool (leaf, branches, fruit, fine root). Note that if '''OK_CLEARCUT''' is used, the model will clearcut at the end of every year in that run. The typical set-up should be: 300 years of spin-up with '''OK_CLEARCUT''' set to FALSE, 1 year with '''OK_CLEARCUT''' set to TRUE, a simulation with the length similar to the age of the forest with '''OK_CLEARCUT''' set to FALSE.  
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     166 
     167++++ CONTINUE CHECKING +++++ 
     168 
    157169 
    158170=== Forest management and management changes (CHECK) ===