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Changes between Version 52 and Version 53 of Documentation/TrunkFunctionality4

Timestamp:: 2020-06-03T18:09:31+02:00 (4 years ago)
Author:: luyssaert
Comment:: --

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Documentation/TrunkFunctionality4

-                      v52
+                      v53
 == Functionalities (alphabetical order) ==
 === Age classes (r6614) ===
 Age classes were introduced to better handle heterogeneity at the landscape level. The feature allows us to distinguish between different successional stages of the same PFT (e.g., a newly grown forest vs. a mature forest). Age classes are independent of the number of diameter classes. Using age classes adds a lot of details to both the biophysics and the biogeochemistry following natural disturbances, forest management and land cover change. If half of a grassland is afforested with a PFT that already exists in the pixel, previous versions of ORCHIDEE will combine this newly forest land and the existing forest in a single PFT. This will result in, for example, a low albedo, a high roughness, and other properties.  When age classes are used, the newly afforested and the existing forest will end up in separate PFTs. One will have a high albedo, the other a low albedo, and other properties may differ significantly as well. In CAN with age classes, PFTs are only merged if the youngest age class for a PFT already has biomass.
+=== Age classes ===
+Describes r6614. Age classes were introduced to better handle heterogeneity at the landscape level. The feature allows us to distinguish between different successional stages of the same PFT (e.g., a newly grown forest vs. a mature forest). Age classes are independent of the number of diameter classes. Using age classes adds a lot of details to both the biophysics and the biogeochemistry following natural disturbances, forest management and land cover change. If half of a grassland is afforested with a PFT that already exists in the pixel, previous versions of ORCHIDEE will combine this newly forest land and the existing forest in a single PFT. This will result in, for example, a low albedo, a high roughness, and other properties.  When age classes are used, the newly afforested and the existing forest will end up in separate PFTs. One will have a high albedo, the other a low albedo, and other properties may differ significantly as well. In CAN with age classes, PFTs are only merged if the youngest age class for a PFT already has biomass.
 Age classes are defined as separate PFTs. Different age classes of the same PFT could therefore be, in principle, run with different parameters. This option has not been tested yet because it is expected to result in discontinuities when the biomass is moved from one age class to another. The number of age classes is fixed for the whole simulation, but for each PFT it can be decided whether age classes are used or not. In other words, if the user chooses four age classes for the simulation, each PFT can have either 1 or 4 age classes.  This adds a lot of flexibility to the model. ORCHIDEE trunk 4, for example, has been run with 64 PFTs, using age classes for European forest and using no age classes for all forests outside the domain of interest. Setting-up a simulation with age classes will require some thinking when creating the orchidee_pft.def. A Python-script was written to create this kind of run.def and is stored in config/ORCHIDEE_OL/MAKE_RUN_DEF. Increasing the number of PFTs has important consequences for the speed of the model and the memory use, although ORCHIDEE trunk 4 does make extensive use of "CYCLE" statements to avoid calculations where no biomass is present. Because a single run can contain PFTs with and PFTs without age classes, processing of the simulation output needs to account for the relationship between PFTs of the same species but a different age class.
 …
 }}}
 === Albedo (r6614) ===
 ORCHIDEE trunk 4 makes use of a two stream radiative transfer scheme through the canopy, extended to multiple canopy levels (https://doi.org/10.5194/gmd-2016-280). The scheme is based on Pinty et al 2006. This approach accounts not only for the leaf mass but also for the vertical and horizontal distribution of the leaf mass (=canopy structure), calculating an effective LAI based on the solar angle. Light from collimated (black sky) and diffuse (white sky) sources are used, and both are weighted equally as information about this partitioning is not yet available in forcing data.  In ORCHIDEE trunk 4 the same scheme is used to simulate the reflected, transmitted and absorbed light, of which the absorbed light as a function of canopy level is passed to the photosynthesis routines and used in place of the exponential LAI layering found in older versions of the TRUNK (see the section Photosynthesis). This implies that albedo and photosynthesis are now fully consistent as well as the light reaching the forest floor (the latter is used in for example recruitment). ORCHIDEE trunk 4 cannot revert to previous approaches for calculating albedo.
+=== Albedo ===
+Describes r6614. ORCHIDEE trunk 4 makes use of a two stream radiative transfer scheme through the canopy, extended to multiple canopy levels (https://doi.org/10.5194/gmd-2016-280). The scheme is based on Pinty et al 2006. This approach accounts not only for the leaf mass but also for the vertical and horizontal distribution of the leaf mass (=canopy structure), calculating an effective LAI based on the solar angle. Light from collimated (black sky) and diffuse (white sky) sources are used, and both are weighted equally as information about this partitioning is not yet available in forcing data.  In ORCHIDEE trunk 4 the same scheme is used to simulate the reflected, transmitted and absorbed light, of which the absorbed light as a function of canopy level is passed to the photosynthesis routines and used in place of the exponential LAI layering found in older versions of the TRUNK (see the section Photosynthesis). This implies that albedo and photosynthesis are now fully consistent as well as the light reaching the forest floor (the latter is used in for example recruitment). ORCHIDEE trunk 4 cannot revert to previous approaches for calculating albedo.
 The radiative transfer through the canopy is controlled by 3 parameters for each wavelength/band: single leaf scattering '''leaf_ssa_xxx''', forward scattering '''leaf_psd_xxx''' and background reflectance '''bgrd_ref_xxx'''. At present, both the visible (VIS) and near-infrared (NIR) spectra have been parameterized. Parameterization is based on running an inverse radiation scheme on the MODIS albedo product while accounting for the different land cover types. The inverted parameters are provided by the JRC as the JRC TIP product. Seasonal variation in the background albedo was observed but small and therefore not accounted for.
 …
 When snow is present in a pixel, all snow is assumed to reach the ground and the background albedo and the snow albedo (calculated as a function of snow age) are weighted according to their cover fractions (see Background albedo).
 === Albedo (background) (r6614) ===
 If covered by snow, the background albedo is calculated in the VIS and NIR wavelengths by the snow module and accounts for snow age and snow density. If not covered by snow, the background albedo is not simulated but prescribed by the parameters '''bgd_reflectance(:,ivis)''' and '''bgd_reflectance(:,inir)'''. If the background is partly covered by snow, the snow albedo and the background albedo are merged, which allows snow to settle under the canopy, reflecting In deciduous forest, grasslands and croplands, the background albedo is known to be strongly affected by the phenology and senescence of the understory vegetation. ORCHIDEE trunk 4 has two options to prescribe the background albedo:
+=== Albedo (background) ===
+Describes r6614. If covered by snow, the background albedo is calculated in the VIS and NIR wavelengths by the snow module and accounts for snow age and snow density. If not covered by snow, the background albedo is not simulated but prescribed by the parameters '''bgd_reflectance(:,ivis)''' and '''bgd_reflectance(:,inir)'''. If the background is partly covered by snow, the snow albedo and the background albedo are merged, which allows snow to settle under the canopy, reflecting In deciduous forest, grasslands and croplands, the background albedo is known to be strongly affected by the phenology and senescence of the understory vegetation. ORCHIDEE trunk 4 has two options to prescribe the background albedo:
 * The background albedo is prescribed per PFT but is constant throughout the year. This option has been evaluated over Europe. Set '''alb_bg_modis''' = n.
 * The background albedo is constant across PFTs. This option reads background maps. Given that those maps are based on the JRC TIP product, they should be compatible with the new albedo scheme. This option, however, has not been evaluated yet. Set '''alb_bg_modis''' = y.
 === Albedo (snow) (r6614) ===
 The snow albedo could be either prescribed (the value of '''fixed_snow_albedo''' should then be set in the run.def and will be read in src_parameters/constantes_var.f90) or calculated following Chalita and Treut (1994) '''ok_snow_albedo_clm3 = n ''' or calculated following CLM3 '''ok_snow_albedo_clm3 = y''' (recommended). The difference between the latter two methods has not been tested yet. The CLM method was implemented in ORCHIDEE-CN-CAN and has been tested in combination with the other changes to the albedo calculations. The Chalita and Treut method was added in parallel to the ORCHIDEE trunk 3.0. When merging both versions, we ended up with two option.
 === Allocation (r6742) ===
 ORCHIDEE trunk 4 uses the allometric allocation as developed in O-CN. In ORCHIDEE trunk 4 the approach was adjusted to work for more than one diameter class. Since it was developed this allocation has been used in ORCHIDEE-CN and ORCHIDEE-CNP. In those branches only a single diameter class was used. Except for the way the reserves and labile pools are calculated (incl. the pseudo sugar loading), the allocation scheme remained rather similar between the aforementioned versions. The model is, however, very sensitive to the way the reserves and labile pools are calculated. The allocation makes use of a labile pool for which the activity is calculated based on the temperature. This sensitivity is important at the start and the end of the growing seasons when temperatures may be low. As such the model addresses the sink/source discussion initiated by Körner. Whereas this approach resulted in an acceptable interannual variability in for example NPP in ORCHIDEE-CAN, adding N seems to have dampen the interannual variability a lot/too much. This dampening was observed in ORCHIDEE-CN  and ORCHIDEE-CN-CAN. IN ORCHIDEE-CNP the temperature relationship was removed (hence NPP and GPP are strictly coupled) because the interannual variability became unrealistic.
+=== Albedo (snow) ===
+Describes r6614. The snow albedo could be either prescribed (the value of '''fixed_snow_albedo''' should then be set in the run.def and will be read in src_parameters/constantes_var.f90) or calculated following Chalita and Treut (1994) '''ok_snow_albedo_clm3 = n ''' or calculated following CLM3 '''ok_snow_albedo_clm3 = y''' (recommended). The difference between the latter two methods has not been tested yet. The CLM method was implemented in ORCHIDEE-CN-CAN and has been tested in combination with the other changes to the albedo calculations. The Chalita and Treut method was added in parallel to the ORCHIDEE trunk 3.0. When merging both versions, we ended up with two option.
+=== Allocation ===
+Describes r6742. ORCHIDEE trunk 4 uses the allometric allocation as developed in O-CN. In ORCHIDEE trunk 4 the approach was adjusted to work for more than one diameter class. Since it was developed this allocation has been used in ORCHIDEE-CN and ORCHIDEE-CNP. In those branches only a single diameter class was used. Except for the way the reserves and labile pools are calculated (incl. the pseudo sugar loading), the allocation scheme remained rather similar between the aforementioned versions. The model is, however, very sensitive to the way the reserves and labile pools are calculated. The allocation makes use of a labile pool for which the activity is calculated based on the temperature. This sensitivity is important at the start and the end of the growing seasons when temperatures may be low. As such the model addresses the sink/source discussion initiated by Körner. Whereas this approach resulted in an acceptable interannual variability in for example NPP in ORCHIDEE-CAN, adding N seems to have dampen the interannual variability a lot/too much. This dampening was observed in ORCHIDEE-CN  and ORCHIDEE-CN-CAN. IN ORCHIDEE-CNP the temperature relationship was removed (hence NPP and GPP are strictly coupled) because the interannual variability became unrealistic.
 There are no options to revert to the allocation based on resource limitation (Friedlingstein et al. 1999). All references and parameters for allocation based on resource limitation have been removed from the code (those that were overlooked can be removed). Allometric allocation makes use of the following PFT-specific parameters: '''sla''', '''longevity_root''', '''longevity_leaf''', '''longevity_sap''', '''pipe_density''', '''tree_ff''', '''pipe_tune_x''', '''k_latosa_max''', and '''k_latosa_min'''. In addition to this set of parameters that mainly describe the allometric relationships and the longevity of the different tissues, the calculation of the allocation coefficients makes use PFT-specific tissue conductivities, i.e., '''k_sap''', '''k_belowground''', and '''k_leaf''' (see also plant water stress). Details on the parameters can be found in the SI of Naudts et al 2015 in GMD or in src_parameters/constantes_mtc.f90.
 …
+=== Anthropogenic species change (r6614) ===
+Following 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.
+=== Bare soil (r6783) ===
+The 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 veget_max_1 + sum(veget_max_i - veget_i) with i from 2 to the number of PFTs. When a deciduous PFT sheds its leaves, the gaps in the forest will thus contribute to the 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 PFT1 deserts as the background albedo of forest gaps. In ORCHIDEE v2.1 the background albedo has been reparameterized and this issue may have been largely resolved now if '''alb_bg_modis''' = y ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/TrunkFunctionality4#Albedobackgroundr6614 more details]). From many points of view a dynamic bare soil fraction is strange, e.g., bare soil has its own water column so when moving the forest gaps from to forest to PFT1 the soil water content, soil carbon content, litter layer, etc all changes temporary. If '''ok_bare_soil_new''' is set to TRUE, canopy gaps no longer contribute to the bare soil. 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 but the calculation of bare soil evaporation underneath a canopy would be problematic. For that reason ok_bare_soil_new is recommended only to be used with the multi-layer energy budget (when run with more than 1 layer). The multi-layer energy budget accounts for within canopy turbulence and can therefore deal with evaporation from beneath a canopy. At present the settings for ok_bare_soil_new are included in the energy_control flag ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/TrunkFunctionality4#Singlevsmultilayerenergybudgetr6614 more details]). The default settings of ORCHIDEE 4.0 combine the new albedo scheme with the single layer energy budget (enerbil) and '''ok_bare_soil_new''' = n.
+=== Bark beetles (r6614) ===
+The 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.
+=== C13 (r6614) ===
+The 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.
+=== Configurations (r6614) ===
+The model comes with the following well-tested configurations (config/ORCHIDEE_OL). Well-tested means that these configuration have been tested on different servers and some are part of the trusting:
+=== Anthropogenic species change ===
+Describes r6614. Following 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.
+=== Bare soil ===
+Describes r6783. The 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 veget_max_1 + sum(veget_max_i - veget_i) with i from 2 to the number of PFTs. When a deciduous PFT sheds its leaves, the gaps in the forest will thus contribute to the 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 PFT1 deserts as the background albedo of forest gaps. In ORCHIDEE v2.1 the background albedo has been reparameterized and this issue may have been largely resolved now if '''alb_bg_modis''' = y ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/TrunkFunctionality4#Albedobackgroundr6614 more details]). From many points of view a dynamic bare soil fraction is strange, e.g., bare soil has its own water column so when moving the forest gaps from to forest to PFT1 the soil water content, soil carbon content, litter layer, etc all changes temporary. If '''ok_bare_soil_new''' is set to TRUE, canopy gaps no longer contribute to the bare soil. 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 but the calculation of bare soil evaporation underneath a canopy would be problematic. For that reason ok_bare_soil_new is recommended only to be used with the multi-layer energy budget (when run with more than 1 layer). The multi-layer energy budget accounts for within canopy turbulence and can therefore deal with evaporation from beneath a canopy. At present the settings for ok_bare_soil_new are included in the energy_control flag ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/TrunkFunctionality4#Singlevsmultilayerenergybudgetr6614 more details]). The default settings of ORCHIDEE 4.0 combine the new albedo scheme with the single layer energy budget (enerbil) and '''ok_bare_soil_new''' = n.
+=== Bark beetles ===
+Describes r6614. The 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.
+=== C13 ===
+Describes r6614. The 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.
+=== Configurations ===
+Describes r6614. The model comes with the following well-tested configurations (config/ORCHIDEE_OL). Well-tested means that these configuration have been tested on different servers and some are part of the trusting:
 * SPINUP: used for single pixel FLUXNET runs.
 * ENSEMBLE: used for single pixel FLUXNET runs ([wiki:Documentation/UserGuide/FLUXNETValidation more details]).
 …
 === Consistency checks (r6614) ===
 The 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.
+=== Consistency checks ===
+Describes r6614. The 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.
 * err_act = 1 is recommended when running global long-term simulations. Under this option, mass balance closure is checked for all biogeochemical processes but only at the highest level thus stomate.f90 and stomate_lpj.f90. Although the mass balance checks are not very expensive in terms of computer time, skipping the numerous lower level checks is expected to save some time. Under this option the total mass balance error is only written to the history file. No information is provided in which subroutine the problem occurred.
 * err_act = 2 is recommended when developing and testing the model. Now the mass balance is explicitly checked in stomate.f90, stomate_lpj.f90 and all its subroutines. Under this option the mass balance error is written to the history file and if the mass balance is not closed, the warning message will indicate in which subroutine the problem likely originated.
 …
 === Croplands (r6614) ===
 Makes use of crop_planting and crop_harvest in the module sapiens_agriculture. Harvest goes into harvest_pool (just like wood) and its decomposition is accounted for in the fluxes from the product use pool.
 === CWRR vs Choinel (r6614) ===
 Following ORCHIDEE trunk 3, the Choinel code is no longer available in ORCHIDEE trunk 4. The hydrological schemes were not touched during the development of ORCHIDEE trunk 4. The hydraulic architecture in ORCHIDEE trunk 4 relies on CWRR.
 === Diameter classes (r6614) ===
 Diameter 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.
+=== Croplands ===
+Describes r6614. Makes use of crop_planting and crop_harvest in the module sapiens_agriculture. Harvest goes into harvest_pool (just like wood) and its decomposition is accounted for in the fluxes from the product use pool.
+=== CWRR vs Choinel ===
+Describes r6614. Following ORCHIDEE trunk 3, the Choinel code is no longer available in ORCHIDEE trunk 4. The hydrological schemes were not touched during the development of ORCHIDEE trunk 4. The hydraulic architecture in ORCHIDEE trunk 4 relies on CWRR.
+=== Diameter classes ===
+Describes r6614. Diameter 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.
 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 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).
 …
 === Forced clear cut (r6614) ===
 '''FORCED_CLEAR_CUT''' 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 '''FORCED_CLEAR_CUT''' 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 '''FORCED_CLEAR_CUT''' set to FALSE, 1 year with '''FORCED_CLEAR_CUT''' set to TRUE, a simulation with the length similar to the age of the forest with '''FORCED_CLEAR_CUT''' set to FALSE.
 === Forest management and management changes (r6614) ===
 % of the global forests are managed, which contradicts the assumption in previous versions of ORCHIDEE that forests are long-lived natural vegetation. Forest management, inspired by ORCHIDEE-FM, was implemented in ORCHIDEE-CAN. Owing to the allometric allocation scheme, the introduction of diameter classes and a canopy structure, only the principles of ORCHIDEE-FM, i.e., the allocation rule of Deleuze and Dhote that allocates carbon to different diameter classes based on the basal area of the tree, and relative-density index (RDI)-based management which enforces thinning and harvest operations based on the current tree density and the self-thinning density, were retained.
+=== Forced clear cut ===
+Describes r6614. '''FORCED_CLEAR_CUT''' 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 '''FORCED_CLEAR_CUT''' 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 '''FORCED_CLEAR_CUT''' set to FALSE, 1 year with '''FORCED_CLEAR_CUT''' set to TRUE, a simulation with the length similar to the age of the forest with '''FORCED_CLEAR_CUT''' set to FALSE.
+=== Forest management and management changes ===
+Describes r6614. 70% of the global forests are managed, which contradicts the assumption in previous versions of ORCHIDEE that forests are long-lived natural vegetation. Forest management, inspired by ORCHIDEE-FM, was implemented in ORCHIDEE-CAN. Owing to the allometric allocation scheme, the introduction of diameter classes and a canopy structure, only the principles of ORCHIDEE-FM, i.e., the allocation rule of Deleuze and Dhote that allocates carbon to different diameter classes based on the basal area of the tree, and relative-density index (RDI)-based management which enforces thinning and harvest operations based on the current tree density and the self-thinning density, were retained.
 The forest management strategy can either be forced as a single value to all PFTs and grid cells, or be read from an input map to allow for spatially and temporally varying strategies.  If the forest management strategy is not specified the default value "unmanaged" (FM = 1) is used. This implies that the stand is never thinned or harvested. Once the stand density drops below the threshold or the tree diameter exceeds a different threshold, a stand replacing disturbance occurs and a new stand is prescribed in the next time step. Therefore, the biomass pools in ORCHIDEE trunk 4 no longer depend on a prescribed longevity.
 …
 === Grasslands (r6614) ===
 In terms of grassland phenology ORCHIDEE trunk 4 follows ORCHIDEE 3.0 as closely as possible. For the moment ORCHIDEE trunk 4 is also using Nicolas's patch that enforces senescence if too many of the leaves are in the oldest leaf age class.  This patch is controlled by the LNVGRASSPATCH flag, and is set to T in the standard run.def.
+=== Grasslands ===
+Describes r6614. In terms of grassland phenology ORCHIDEE trunk 4 follows ORCHIDEE 3.0 as closely as possible. For the moment ORCHIDEE trunk 4 is also using Nicolas's patch that enforces senescence if too many of the leaves are in the oldest leaf age class.  This patch is controlled by the LNVGRASSPATCH flag, and is set to T in the standard run.def.
 Part of the turnover goes into the harvest pool (harvest_fraction is now hard coded to 0.5 for sapwood and leaves and 0 for roots in stomate_turnover.f90 - see ticket #687). This simple parameter should be replaced by a grassland management module but for the moment 50% of the turnover goes into the harvest_pool (just like wood) and its decomposition is accounted for in the fluxes from the product use pool.
 === Harvest (r6614) ===
 All biomass harvest is recorded in a harvest variable '''harvest_pool''', this variable also stores the mass and dimensions of the harvest/mortality (absolute numbers thus accounting for the pixel area!). Related variables were introduced: '''harvest_type''', '''harvest_cut''', and '''harvest_area'''. Wood product pools and fluxes from wood and biomass decomposition are calculated in a separate module dedicated to wood use. The dimension of the wood use pools were externalized and can be changed to better address regional differences when aiming for regional simulations. The default 1, 10 and 100 year pools were replaced by 2, 17 and 50 years which is closer to the reality for Europe. For most parts of the world a 100 year wood pool is very optimistic.
 === Leaf area index map (r6614) ===
 Four flags have been identified that control the model behavior in terms of lai: '''ok_stomate''', '''ok_pheno''', '''impveg''' and '''read_lai'''. There is a 5th implicit flag which is whether restart files are used or not. If a restart file is used, the lai values will come from the sechiba restart file which is read at t=48. Given that each flag can take two values, we have 32 configurations in total. Out of these 32 configurations 10 are defined of which about 5 to 7 seem to be intended (for more details see '''Start and restart - Table 1'''). Many of the remaining 22 settings are inconsistent (i.e. running stomate to calculate a lai and reading an lai_map to prescribe lai), duplicate other settings, or would require further developments to work properly. Furthermore, the current code does not stop or warn when inconsistent settings are selected. The table (see Start and restart) proposes a scheme with 2 flags which can run with our without restart files, thus resulting in 8 different ways to control the lai in sechiba or the initial lai in stomate. The remaining 2 combinations are inconsistent and will stop the model.
+=== Harvest ===
+Describes r6614. All biomass harvest is recorded in a harvest variable '''harvest_pool''', this variable also stores the mass and dimensions of the harvest/mortality (absolute numbers thus accounting for the pixel area!). Related variables were introduced: '''harvest_type''', '''harvest_cut''', and '''harvest_area'''. Wood product pools and fluxes from wood and biomass decomposition are calculated in a separate module dedicated to wood use. The dimension of the wood use pools were externalized and can be changed to better address regional differences when aiming for regional simulations. The default 1, 10 and 100 year pools were replaced by 2, 17 and 50 years which is closer to the reality for Europe. For most parts of the world a 100 year wood pool is very optimistic.
+=== Leaf area index map ===
+Describes r6614. Four flags have been identified that control the model behavior in terms of lai: '''ok_stomate''', '''ok_pheno''', '''impveg''' and '''read_lai'''. There is a 5th implicit flag which is whether restart files are used or not. If a restart file is used, the lai values will come from the sechiba restart file which is read at t=48. Given that each flag can take two values, we have 32 configurations in total. Out of these 32 configurations 10 are defined of which about 5 to 7 seem to be intended (for more details see '''Start and restart - Table 1'''). Many of the remaining 22 settings are inconsistent (i.e. running stomate to calculate a lai and reading an lai_map to prescribe lai), duplicate other settings, or would require further developments to work properly. Furthermore, the current code does not stop or warn when inconsistent settings are selected. The table (see Start and restart) proposes a scheme with 2 flags which can run with our without restart files, thus resulting in 8 different ways to control the lai in sechiba or the initial lai in stomate. The remaining 2 combinations are inconsistent and will stop the model.
 In previous ORCHIDEE trunks, canopy structure is prescribed by a single variable called lai and the assumption of a turbid medium (Lambert-Beer). Consequently reading an lai value suffice to prescribe the entire canopy. In ORCHIDEE trunk 4, however, canopy structure has become a 3D property that can be calculated from the leaf biomass, stem biomass, the number of individuals and the assumptions that the trees follow a Poisson distribution in the horizontal plain, that the crowns are spherical and that the leaf biomass is uniformly distributed within the crowns.
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 === Land cover change (with age classes) (r6614) ===
 Land cover change now accounts for age classes. It is controlled by '''veget_update'''. Set '''veget_update''' = 0Y if land cover change should be disabled. The wood pool and its subsequent fluxes were moved from the land cover change routine to a separate routine. Furthermore, land cover change also deals with the change of biological land uses to non biological land uses (of which the most important change is probably urbanization). If urbanization happens, all the carbon an nitrogen are stored in a series of variables '''burried_xxx''' where xxx stands for a different pool, e.g., litter, soil, .... Burried_xxx are cumulative variables thus increasing over time . There is a place holder in sapiens_lcchange.90 to also develop the release of the buried carbon and nitrogen following de-urbanization (see ticket #616). The series of the burried_xxx variables are not yet written to an output file but this could be easily added (they are already defined in the xml files).
+=== Land cover change (with age classes) ===
+Describes r6614. Land cover change now accounts for age classes. It is controlled by '''veget_update'''. Set '''veget_update''' = 0Y if land cover change should be disabled. The wood pool and its subsequent fluxes were moved from the land cover change routine to a separate routine. Furthermore, land cover change also deals with the change of biological land uses to non biological land uses (of which the most important change is probably urbanization). If urbanization happens, all the carbon an nitrogen are stored in a series of variables '''burried_xxx''' where xxx stands for a different pool, e.g., litter, soil, .... Burried_xxx are cumulative variables thus increasing over time . There is a place holder in sapiens_lcchange.90 to also develop the release of the buried carbon and nitrogen following de-urbanization (see ticket #616). The series of the burried_xxx variables are not yet written to an output file but this could be easily added (they are already defined in the xml files).
 An interesting parameter is '''min_vegfrac'''. When reading in a land cover map, PFTs with a fraction below min_vegfrac are removed. Likewise the fraction cover of a PFT after a land cover change should not be less than min_vegfrac either. This requirement seems to have been solely established to avoid ending up with too many PFTs with very small fractions. Because the the non-biological and biological fraction covers of each pixel should sum up to one, removing even these very small fractions implies that these fractions need to be added to one of the remaining PFTs. First it is tried to add the fraction to the bare soil (this will only be accepted if the new fraction of the bare soil exceeds min_vegfrac), then the code tries to allocate the residual fraction to the largest vegetated fraction. If age classes are used this should be the largest vegetated fraction in the first age class of a PFT. If all of the above failed, the residual fraction is added to frac_nobio irrespective of whether frac_nobio exceeds min_vegfrac. Everytime this happens, the failure to meet the min_vegfrac criterion is registered in the variable '''failed_vegfrac'''. This variable is not yet added to an output file.
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 Note that the min_vegfrac criterion could be the reason of why very small land cover changes occur. Another consequence is that the land cover fractions in the model are not exactly the same as those read in from the maps. Deviations should remain small and should not accumulate over time. Assume that in y0 the fraction of PFT2 = 0. In y1 the map tells us the fraction is half of min_vegfrac. The model will keep the PFT fraction to zero. The model and the map will no longer be in line with each other. In y2 the map tells us the fraction is twice min_vegfrac. The model will now accept the change. The model and the map will be in line with each other.
 === Litter decomposition (r6614) ===
 After large-scale dieback events (with a closed n-cycle, i.e., impose_cn = n), so much soil mineral N becomes immobilized to decompose litter that too little N is left for plant regrowth. To address this, we implicitly represent the action of fungivores, which eat the decomposing fungi and release N for the plants and increase N turnover rates. We set aside a fraction of qd (stomate_litter.f90) which becomes available for plant uptake in nitrogen_dynamics. This fraction is calculated and is at its maximum when the litter pool is large compared to the biomass pool. The fraction is at its lowest when the living biomass is high compared to the litter biomass. The implemented principle mimics a Lokta-Volta dynamic where the predator are the fungivores and the prey the fungi. The share of the N contained in the decomposing fungi that is released as an excrement from the fungivores ranges between 0 and 1 and is calculated.
+=== Litter decomposition ===
+Describes r6614. After large-scale dieback events (with a closed n-cycle, i.e., impose_cn = n), so much soil mineral N becomes immobilized to decompose litter that too little N is left for plant regrowth. To address this, we implicitly represent the action of fungivores, which eat the decomposing fungi and release N for the plants and increase N turnover rates. We set aside a fraction of qd (stomate_litter.f90) which becomes available for plant uptake in nitrogen_dynamics. This fraction is calculated and is at its maximum when the litter pool is large compared to the biomass pool. The fraction is at its lowest when the living biomass is high compared to the litter biomass. The implemented principle mimics a Lokta-Volta dynamic where the predator are the fungivores and the prey the fungi. The share of the N contained in the decomposing fungi that is released as an excrement from the fungivores ranges between 0 and 1 and is calculated.
 After a die-back (with a closed n-cycle, i.e., impose_cn = n) too little N is available to reach the target C:N ratio of the receiving soil pool, meaning that carbon litter cannot decompose. If the C:N ratio is not controlled it spins out of control reaching values of more than 600. The target C:N ratio, which is a variable in stomate_litter.f90, can now vary between 1 and '''max_cn''' where the latter can be set in the run.def. Good results were obtained by setting max_cn to 250. max_cn is bound between 1 and 400, the C:N ratio of wood which is the pool with the highest C:N ratio (and biomass that contributes to the litter). During the simulation the target C:N ratio varies and a couple of decades after the dieback reaches the expected value between 5 and 20. The ecological justification behind a max_cn above the C:N ratio of the fungi is that mycorrhizae receive their C from the plant photosynthesis products. Thus, litter can still decompose even though C is not incorporated into the plant biomass. max_cn can be set in the run.def:
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 === Litter raking (r6614) ===
 Tree litter was collected from the forest and used in the winter in stables instead of straw. In spring the litter and manure was spread on the croplands. This lateral flow of C and N between PFTS in the same pixel can be accounted for in ORCHIDEE trunk 4 by setting '''use_litter_raking''' = y. If litter raking is to be used, the model will search for annual maps. The path of these maps needs to be specified in COMP/stomate.card. Litter raking maps were prepared for Europe. Unless liter raking is your research topic set '''use_litter_raking''' = n. An example of to set up the model to make use of the historical litter raking maps can be found in config/ORCHIDEE_OL/OOL_SEC_STO_FG4
 === Litter resistance to evaporation (r6783) ===
 The default for the flag '''do_rsoil''' has changed to TRUE. When set to TRUE the flag reduces the bare soil evaporation because it accounts for the moisture content of the litter layer (Sellers et al., 1992). The presence of litter always acts as an extra barrier (resistance) to bare soil evaporation. If the litter layer dries out the resistance will even further increase. As in previous version, ORCHIDEE 4 calculates the bare soil fraction as PFT1 + SUM(veget_max_i - veget_i) where i goes from 2 to the number of PFTs. veget is now calculated by using Pgap which resulted in more bare soil, the extra resistance from litter helps to keep to evapotranspiration in check.
 === Mortality (r6614) ===
 ORCHIDEE trunk 4 distinguishes 2 types of natural mortality: (1) explicitly considering mortality from disturbances and self-thinning, and (2) implicitly considering background mortality. Ideally, approach (1) should be further developed such that all underlying agents driving background mortality are represented in the model (i.e., gap-scale mortality, pests, disease, windthrow, etc.) such that it can replace approach (2). Two options of background mortality may be chosen: constant background mortality and dynamic background mortality. To use the first option, set the flag '''constant_mortality''' = y. The background mortality of a forests is calculated as a constant, prescribed fraction. In trunk 4, this fraction is given by '''residence_time''' (see also forest management). Otherwise set '''constant_mortality''' = n, the dynamic background mortality of a forest is a function of its net primary production (npp). If npp decreases, mortality will increase Both options have been developed but only '''constant_mortality''' = y has been tested in ORCHIDEE trunk 4.
+=== Litter raking ===
+Describes r6614. Tree litter was collected from the forest and used in the winter in stables instead of straw. In spring the litter and manure was spread on the croplands. This lateral flow of C and N between PFTS in the same pixel can be accounted for in ORCHIDEE trunk 4 by setting '''use_litter_raking''' = y. If litter raking is to be used, the model will search for annual maps. The path of these maps needs to be specified in COMP/stomate.card. Litter raking maps were prepared for Europe. Unless liter raking is your research topic set '''use_litter_raking''' = n. An example of to set up the model to make use of the historical litter raking maps can be found in config/ORCHIDEE_OL/OOL_SEC_STO_FG4
+=== Litter resistance to evaporation ===
+Describes r6783. The default for the flag '''do_rsoil''' has changed to TRUE. When set to TRUE the flag reduces the bare soil evaporation because it accounts for the moisture content of the litter layer (Sellers et al., 1992). The presence of litter always acts as an extra barrier (resistance) to bare soil evaporation. If the litter layer dries out the resistance will even further increase. As in previous version, ORCHIDEE 4 calculates the bare soil fraction as PFT1 + SUM(veget_max_i - veget_i) where i goes from 2 to the number of PFTs. veget is now calculated by using Pgap which resulted in more bare soil, the extra resistance from litter helps to keep to evapotranspiration in check.
+=== Mortality ===
+Describes r6614. ORCHIDEE trunk 4 distinguishes 2 types of natural mortality: (1) explicitly considering mortality from disturbances and self-thinning, and (2) implicitly considering background mortality. Ideally, approach (1) should be further developed such that all underlying agents driving background mortality are represented in the model (i.e., gap-scale mortality, pests, disease, windthrow, etc.) such that it can replace approach (2). Two options of background mortality may be chosen: constant background mortality and dynamic background mortality. To use the first option, set the flag '''constant_mortality''' = y. The background mortality of a forests is calculated as a constant, prescribed fraction. In trunk 4, this fraction is given by '''residence_time''' (see also forest management). Otherwise set '''constant_mortality''' = n, the dynamic background mortality of a forest is a function of its net primary production (npp). If npp decreases, mortality will increase Both options have been developed but only '''constant_mortality''' = y has been tested in ORCHIDEE trunk 4.
 However, because of the introduction of self-thinning in ORCHIDEE trunk 4, '''constant_mortality''' = y became the default setting. In ORCHIDEE trunk 4, the total mortality is the maximum of the background mortality and the mortality from self-thinning. Only if self-thinning is absent or too low, background mortality will play a role. This approach implies that when '''constant_mortality''' = y is used in combination with self-thinning, background mortality will only play a role in the first years to decade before self-thinning starts (the latest calculations of RDI - see Prescribe - the role of the background mortality has further decreased). Despite its limited use, it represents an essential process: owing to background mortality, the number of individuals decreases, the remaining individuals grow faster and thus manage to reach self-thinning in a reasonable amount of time.
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 === Nitrogen cycle (r6614) ===
 ORCHIDEE trunk 4 strictly follows ORCHIDEE trunk 3 where it concerns the implementation of the N-cycle. Following mass balance problems caused by negative N mineralization and followed by negative immobilization, the code has been slightly adjusted to ensure mass balance closure. First the flag '''stomate_ok_ncycle''' needs to be set to y, to run the model with a N-cycle. Subsequently the parameter '''impose_cn''' is used to control the N-cycle calculations. If set to y, C/N ratios are calculated but whenever N appears to be limiting, it is taken from the atmosphere to satisfy this need. This is the preferred setting when testing/developing the code without a proper spin-up. N-limitation will only be accounted for when setting impose_cn = n. With this setting the N-cycle is closed (checked when checking for mass balance closure) it requires a spin-up to produce reasonable results.
+=== Nitrogen cycle ===
+Describes r6614. ORCHIDEE trunk 4 strictly follows ORCHIDEE trunk 3 where it concerns the implementation of the N-cycle. Following mass balance problems caused by negative N mineralization and followed by negative immobilization, the code has been slightly adjusted to ensure mass balance closure. First the flag '''stomate_ok_ncycle''' needs to be set to y, to run the model with a N-cycle. Subsequently the parameter '''impose_cn''' is used to control the N-cycle calculations. If set to y, C/N ratios are calculated but whenever N appears to be limiting, it is taken from the atmosphere to satisfy this need. This is the preferred setting when testing/developing the code without a proper spin-up. N-limitation will only be accounted for when setting impose_cn = n. With this setting the N-cycle is closed (checked when checking for mass balance closure) it requires a spin-up to produce reasonable results.
 The paths of the N-inputs from atmospheric N-deposition, fertilization, and biological nitrogen fixation ('''Nammonium_FILE''', '''Nnitrate_FILE''', '''Nfert_FILE''' , '''NManure_FILE''' and '''Nbnf_FILE''') are set in the stomate.card. Moreover, the N inputs you wish to include in your simulation can be specified in the run.def. If set to NONE, the given N input files will not be read.
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 === Parameter files (r6614) ===
 A model run now requires three different parameter files: run.def, orchidee.def and orchidee_pft.def. LibIGCM reads these files in COMP/orchidee_ol.card.
+=== Parameter files ===
+Describes r6614. A model run now requires three different parameter files: run.def, orchidee.def and orchidee_pft.def. LibIGCM reads these files in COMP/orchidee_ol.card.
 * The run.def contains all the information for the driver. This is also the file where the default global domain can be reduced (LIMIT_N, LIMIT_S, LIMIT_E and LIMIT_W). When the same experiment is to run in off-line and coupled mode, only the run.def should be changed.
 * The orchidee.def contains the details of the experiment together with the settings of the orchidee_ol, sechiba and stomate cards in COMP. Each of the predefined configurations in config/ORCHIDEE_OL will have different settings. These files need to set up manually because each experiment will differ. Copy the best matching predefined experiment from config/ORCHIDEE_OL and use it as a template to set-up your own simulation experiment.
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 === Phenology (r6614) ===
 The pft-specific parameter '''always_init''' controls whether the phenology depends on the reserves (set to .FALSE.) or is forced (set to .TRUE.). Note that a forced phenology (thus always_init = .TRUE.) has no ecophysiological basis, it is a numerical approach to stabilize the vegetation cover. A stable vegetation cover is particularly welcome in coupled simulations but likely hides real vegetation dynamics (especially under future climate conditions) or problems in other routines or parameter settings. If a PFT keeps dying in an area where it is currently present, this would hint at a problem with the current model/parameters. If a PFT keeps dying under future conditions, it may be a real response (depending on the PFT). If forced phenology is used, plants will develop an initial canopy in phenology irrespective of whether the plant had sufficient carbon and nitrogen reserves and for evergreen species irrespective of whether the canopy was viable at all. This setting basically overcomes a mortality event at the expense of taking up carbon and nitrogen from the atmosphere. When used in combination with impose_cn = n, an inconsistency is introduced: impose_cn = n reflect the desire to close the nitrogen cycle, always_init = y opens a backdoor in the nitrogen cycle.
+=== Phenology ===
+Describes r6614. The pft-specific parameter '''always_init''' controls whether the phenology depends on the reserves (set to .FALSE.) or is forced (set to .TRUE.). Note that a forced phenology (thus always_init = .TRUE.) has no ecophysiological basis, it is a numerical approach to stabilize the vegetation cover. A stable vegetation cover is particularly welcome in coupled simulations but likely hides real vegetation dynamics (especially under future climate conditions) or problems in other routines or parameter settings. If a PFT keeps dying in an area where it is currently present, this would hint at a problem with the current model/parameters. If a PFT keeps dying under future conditions, it may be a real response (depending on the PFT). If forced phenology is used, plants will develop an initial canopy in phenology irrespective of whether the plant had sufficient carbon and nitrogen reserves and for evergreen species irrespective of whether the canopy was viable at all. This setting basically overcomes a mortality event at the expense of taking up carbon and nitrogen from the atmosphere. When used in combination with impose_cn = n, an inconsistency is introduced: impose_cn = n reflect the desire to close the nitrogen cycle, always_init = y opens a backdoor in the nitrogen cycle.
 From a conceptual point of view, ORCHIDEE trunk 4 is all about vegetation dynamics and thus instabilities in the vegetation cover. In ORCHIDEE trunk 4 there are two processes that can deal with dying PFts including evergreens PFTs. First, ok_recruitment could used. If ok_recruitment = .TRUE. a decrease in the canopy cover will result in more light reaching the forest floor which in turn should trigger recruitment of -for the moment- the same PFT. Generation can take over from each other without loosing the canopy cover entirely. Second, if there are insufficient reserves to grow no leaves, there will be no or insufficient gpp, the carbon reserves will be consumed by respiration processes, the plants will be killed, the biomass transferred to the litter pools and the same or another PFT (see section on species change) will be replanted. ORCHIDEE trunk 4 was developed to work with always_init = .FALSE. so this has become the default value, contrary to previous versions of the trunk where always_init = .TRUE. is the default.
 === Photosynthesis (r6614) ===
 Photosynthesis is calculated as in ORCHIDEE trunk 4, and ORCHIDEE trunk 3 but the way the canopy levels are defined has changed. The reason of this change is in the albedo and energy budget for which physical layers are required. For this reason the space between the bottom and the top of the canopy is divided into x layers. x is set by the parameter '''nlevels_photo'''. Applications with ORCHIDEE trunk 4 used nlevels_photo = 10. Contrary to previous trunk versions of ORCHIDEE where each canopy layer contained 0.5 units of LAI, in ORCHIDEE trunk 4, each canopy layer will have the same depth (in m) but will contain a different amount of LAI because tree canopies are assumed spherical.
 === Plant water stress (r6614) ===
 With ORCHIDEE trunk 4 there are two option to calculate waters stress:
+=== Photosynthesis ===
+Describes r6614. Photosynthesis is calculated as in ORCHIDEE trunk 4, and ORCHIDEE trunk 3 but the way the canopy levels are defined has changed. The reason of this change is in the albedo and energy budget for which physical layers are required. For this reason the space between the bottom and the top of the canopy is divided into x layers. x is set by the parameter '''nlevels_photo'''. Applications with ORCHIDEE trunk 4 used nlevels_photo = 10. Contrary to previous trunk versions of ORCHIDEE where each canopy layer contained 0.5 units of LAI, in ORCHIDEE trunk 4, each canopy layer will have the same depth (in m) but will contain a different amount of LAI because tree canopies are assumed spherical.
+=== Plant water stress ===
+Describes r6614. With ORCHIDEE trunk 4 there are two option to calculate waters stress:
 * Same as in ORCHIDEE 3.0 and previous ORCHIDEE trunks, where a soil moisture stress functions limits C assimilation through constraints on the carboxylation capacity.
 * The second possibility takes hydraulic architecture of plants into account, when calculating the plant water supply. This scheme, based on Hickler et al (2006), calculates the water supply as the ratio of the pressure difference between the soil and leaves. The plant water supply is the amount of  water the plant can transport from the soil to the stomate accounting for resistance of water transport in the roots, sapwood and leaves. The resistances are inversely proportional to the conductivities in these different tissues, with the sapwood conductivity decreasing when cavitation occurs. If transpiration rates exceeds plant water supply, stomatal conductance is reduced. If you wish to make simulations with the hydraulic architecture choose the correct setting for '''energy_control''' (see section on Single layer vs. multi-layer energy budget for more elaboration on these flags).
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 === Prescribe initial vegetation (r6614) ===
 At the start of the model run or after a die-back or clear-cut new vegetation needs to be planted as ORCHIDEE does not grow vegetation from seeds. The initial dimensions of the vegetation are thus prescribed. Given that the allocation follows allometric relationships, any of the tree dimensions or any mass of any component could have been used to prescribe. The variable diameter was chosen because it is easy to (mentally) visualize the prescribed vegetation. In the run.def  '''dia_init_min''' and '''dia_init_max''' need to be prescribed. Typical values are 1 to 3 cm. If more than one diameter class is used, '''dia_init_max ''' needs to larger than '''dia_init_min'''. The larger the difference between the min and max, the more vegetation layers the canopy will be composed from. Grasses are prescribed by the parameters '''height_init_min''' and '''height_init_max''' because we have no diameter-height relationship for grasses. Note that '''height_init_min''' and '''height_init_max''' are the same. The fact that we have two values is a left over from previous versions of stomate_prescribe.f90 (see ticket #688).
+=== Prescribe initial vegetation ===
+Describes r6614. At the start of the model run or after a die-back or clear-cut new vegetation needs to be planted as ORCHIDEE does not grow vegetation from seeds. The initial dimensions of the vegetation are thus prescribed. Given that the allocation follows allometric relationships, any of the tree dimensions or any mass of any component could have been used to prescribe. The variable diameter was chosen because it is easy to (mentally) visualize the prescribed vegetation. In the run.def  '''dia_init_min''' and '''dia_init_max''' need to be prescribed. Typical values are 1 to 3 cm. If more than one diameter class is used, '''dia_init_max ''' needs to larger than '''dia_init_min'''. The larger the difference between the min and max, the more vegetation layers the canopy will be composed from. Grasses are prescribed by the parameters '''height_init_min''' and '''height_init_max''' because we have no diameter-height relationship for grasses. Note that '''height_init_min''' and '''height_init_max''' are the same. The fact that we have two values is a left over from previous versions of stomate_prescribe.f90 (see ticket #688).
 In addition, the initial number of seedlings needs to be prescribed as well. For this a parameter needs to be set. This is a critical parameter to obtain acceptable model behaviour. If it is too high, lai saturates but the stand-level GPP will be distributed over too many individuals, each individual will grow very little and so it will take very long before self-thinning is reached. If it is set too low, LAI will be too low resulting in a too low GPP and thus very slow growth. A good starting values is a bit below self-thinning. That way the vegetation starts growing, individual are killed thanks to the background mortality and within 10 to 20 years self-thinning is reached. Why not starting at self-thinning? During code development it was tried to have the model start at the exact number of trees at which self-thinning will start given the diameter of the tree. One issues was that when prescribing small individuals (1 to 3
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 === Pseudo sugar loading (r6614) ===
 The model code does not control the C/N ratio of the labile pool hence, even if there is a strong N-limitation, the model can accumulate lots of carbon in the labile pool. The first CN-version was indeed doing this as the plant could easily store several 1000 gC m-2. As this was considered unrealistic, the excess C in the labile pool was burned-off by some excess respiration. Although this luxury/wastage respiration has been suggested in the literature (see Amthor et al 2000 and Chamber et al 2004) it is not confirmed by many observations. It was therefore decided to control the size of the labile pool. The model already had an estimate of the optimal pool size of the labile and carbres pools. If the plant has more labile carbon than the optimal, GPP is downregulated because too much sugars in the leaves will increase the viscosity and hamper the sapflow in the phloem. The viscosity can be decreased again by closing the stomata and transpiring less of the sapflow in the xylem. By closing the stomata, GPP will be downregulated (Holtta et al 2017 doi:10.1093/treephys/tpx011). Because ORCHIDEE has no sapflow, turgor and viscosity yet, we used a simple ratio to downregulate NUE. Hence, the feature was called '''pseudo sugar loading''' to make clear this is not the real thing yet.
+=== Pseudo sugar loading ===
+Describes r6614. The model code does not control the C/N ratio of the labile pool hence, even if there is a strong N-limitation, the model can accumulate lots of carbon in the labile pool. The first CN-version was indeed doing this as the plant could easily store several 1000 gC m-2. As this was considered unrealistic, the excess C in the labile pool was burned-off by some excess respiration. Although this luxury/wastage respiration has been suggested in the literature (see Amthor et al 2000 and Chamber et al 2004) it is not confirmed by many observations. It was therefore decided to control the size of the labile pool. The model already had an estimate of the optimal pool size of the labile and carbres pools. If the plant has more labile carbon than the optimal, GPP is downregulated because too much sugars in the leaves will increase the viscosity and hamper the sapflow in the phloem. The viscosity can be decreased again by closing the stomata and transpiring less of the sapflow in the xylem. By closing the stomata, GPP will be downregulated (Holtta et al 2017 doi:10.1093/treephys/tpx011). Because ORCHIDEE has no sapflow, turgor and viscosity yet, we used a simple ratio to downregulate NUE. Hence, the feature was called '''pseudo sugar loading''' to make clear this is not the real thing yet.
 The regulation is smoothened by setting boundaries to avoid sudden decreases in GPP (which are not apparent in the data). Smoothing is taken care of in stomate_vmax.f90. If the plant has less carbon in its labile and carbres pools than wanted, the NUE is upregulated. Up regulation is also capped to avoid crazy NUE values and high frequency changes between up and downregulation. Up and downregulation are done in stomate_vmax.f90. The parameters than control the smoothing are '''sugar_load_min''' and '''sugar_load_max''' and can be set in the run.def.
 === Recruitment (r6614) ===
 When stands grow old the tree density decreases and under certain conditions the LAI can no longer cover the ground area. When this happens productivity will start to decrease. In nature the decrease in LAI comes with an increase in the amount of light reaching the forest floor which enables seedlings to grow and to restore the LAI. This process is known as recruitment. Note that in managed forest and forest with a lot of stand replacing disturbances (for example, fire) the forest may never reach the stage where the canopy sufficiently opens up to enable recruitment.
+=== Recruitment ===
+Describes r6614. When stands grow old the tree density decreases and under certain conditions the LAI can no longer cover the ground area. When this happens productivity will start to decrease. In nature the decrease in LAI comes with an increase in the amount of light reaching the forest floor which enables seedlings to grow and to restore the LAI. This process is known as recruitment. Note that in managed forest and forest with a lot of stand replacing disturbances (for example, fire) the forest may never reach the stage where the canopy sufficiently opens up to enable recruitment.
 ORCHIDEE trunk 4 can simulate recruitment for each PFT separately by setting '''recruitment_pft''' to true or false. When using age classes it makes sense to have the same setting for all age classes of the same species. When developing and testing the code it was considered too time consuming to change the settings at the PFT level so a flag ignoring the setting for recruitment_pft was introduced. If the '''ok_recruitment''' flag is set to true, the settings of recruitment_pft will be used. If the '''ok_recruitment''' flag is set to false, the settings of recruitment_pft will be ignored and the model runs without recruitment.
 …
 === River routing (r6614) ===
 This functionality works has not been evaluated yet for ORCHIDEE trunk 4, although it technically runs. Unless rivers are your main interest, set '''river_routing''' to n. The functionality still has problem when combined with the zoomed grids because pixels far away from the zoom become so big that some rivers can no longer reach the sea. Stand alone applications of ORCHIDEE trunk 4 with river routing being activated require that the whole watershed in include in the simulation domain. If not the model will crash right at the start.
 === run.def (r6614) ===
 The format of the run.def has been modified to use the same structure for both coupled and off-line runs.  The run.def is split between its driver settings (written in run.def), general items which control the ORCHIDEE model (in the orchidee.def file), and PFT-dependent parameters (in the orchidee_pft.def file). A script is now included with the config/ORCHIDEE_OL directory called MAKE_RUN_DEF. This scripts generates different orchidee_pfts.def files. Default model configurations (and thus different orchidee.def files) can be found in config/ORCHIDEE_OL.
+=== River routing ===
+Describes r6614. This functionality works has not been evaluated yet for ORCHIDEE trunk 4, although it technically runs. Unless rivers are your main interest, set '''river_routing''' to n. The functionality still has problem when combined with the zoomed grids because pixels far away from the zoom become so big that some rivers can no longer reach the sea. Stand alone applications of ORCHIDEE trunk 4 with river routing being activated require that the whole watershed in include in the simulation domain. If not the model will crash right at the start.
+=== run.def ===
+Describes r6614. The format of the run.def has been modified to use the same structure for both coupled and off-line runs.  The run.def is split between its driver settings (written in run.def), general items which control the ORCHIDEE model (in the orchidee.def file), and PFT-dependent parameters (in the orchidee_pft.def file). A script is now included with the config/ORCHIDEE_OL directory called MAKE_RUN_DEF. This scripts generates different orchidee_pfts.def files. Default model configurations (and thus different orchidee.def files) can be found in config/ORCHIDEE_OL.
 If one is interested in running two identical simulations with the land-only and the land-atmosphere model, only the run.def needs to be replaced. If one is interested in running the model in the same mode (land-only or land-atmosphere) but change the model functionality, only orchidee.def needs to be changed. If one is interested in running the same mode and same model functionality but only wants to change the PFTs tho orchidee_pft.def file will have to be changed. This modularity is expected to enhance the transparency of the model configuration.
 === Soil maps (r6614) ===
 ORCHIDEE trunk 4 runs for two soil maps: zobler (3 soil types) and usda (12 soil types). Although the usda map has been the default for a while, ORCHIDEE trunk 4 is back at using Zobler due to yet to resolve issues with the usda map. The code has been adjusted in hydraulic_architect.f90 and stomate_windthrow.f90 so it works with Zobler and usda. The soil map can be selected run.def by setting the value for '''soiltype_classif''':
+=== Soil maps ===
+Describes r6614. ORCHIDEE trunk 4 runs for two soil maps: zobler (3 soil types) and usda (12 soil types). Although the usda map has been the default for a while, ORCHIDEE trunk 4 is back at using Zobler due to yet to resolve issues with the usda map. The code has been adjusted in hydraulic_architect.f90 and stomate_windthrow.f90 so it works with Zobler and usda. The soil map can be selected run.def by setting the value for '''soiltype_classif''':
 {{{
 SOILTYPE_CLASSIF= usda
 …
 === Single vs multi layer energy budget (r6614) ===
 There are still some issues with the multi-layer energy budget, and it is currently only possible to run for one PFT. Thus, we suggest you use the single layer energy budget. In this can, however, be done by two different methods that in theory should give the exact same results:
+=== Single vs multi layer energy budget ===
+Describes r6614. There are still some issues with the multi-layer energy budget, and it is currently only possible to run for one PFT. Thus, we suggest you use the single layer energy budget. In this can, however, be done by two different methods that in theory should give the exact same results:
 A - Use the energy scheme as found in the original enerbil.f90
 B - Use the multi-layer energy scheme for a single canopy layer. This should reduce the multi-layer energy scheme to the original enerbil code but this is no longer the case in r6614. This needs to be restored (see ticket #276, #379, #457)
 …
 === Specific leaf area (r6614) ===
 Similar to ORCHIDEE 3.0, ORCHIDEE trunk 4 users can choose to use a constant specific leaf area (SLA) or a dynamic (SLA) by setting the flag '''dyn_sla'''. SLA is a fundamental parameter in the allocation scheme and it is well established that SLA is dynamic in nature especially during leaf onset. Nevertheless, the effect of this flag is much more limited than one could expect based on the perceived importance of sla.
 === Spin-up (r6614) ===
 The analytical spin-up works with ORCHIDEE trunk 4. To ensure growth at the onset of the analytic spin-up for all PFTs initial values are needed for the SOM pools, and that is  irrespective of whether IMPOSE_CN is y or n. The initial pools are set in stomate_io.f90, and they can be specified in the run.def by:
+=== Specific leaf area ===
+Describes r6614. Similar to ORCHIDEE 3.0, ORCHIDEE trunk 4 users can choose to use a constant specific leaf area (SLA) or a dynamic (SLA) by setting the flag '''dyn_sla'''. SLA is a fundamental parameter in the allocation scheme and it is well established that SLA is dynamic in nature especially during leaf onset. Nevertheless, the effect of this flag is much more limited than one could expect based on the perceived importance of sla.
+=== Spin-up ===
+Describes r6614. The analytical spin-up works with ORCHIDEE trunk 4. To ensure growth at the onset of the analytic spin-up for all PFTs initial values are needed for the SOM pools, and that is  irrespective of whether IMPOSE_CN is y or n. The initial pools are set in stomate_io.f90, and they can be specified in the run.def by:
 {{{
 SOM_INIT_ACTIVE = 1000
 …
 === Start and restart (r6614) ===
 The table below shows typical configurations to start and restart ORCHIDEE trunk 4
+=== Start and restart ===
+Describes r6614. The table below shows typical configurations to start and restart ORCHIDEE trunk 4
 || '''Sechiba''' || || || || '''stomate''' || || ||
 || '''Restart''' || '''impveg''' || '''impsoil''' || '''laimap''' || '''ok_stomate''' || '''restart''' || '''Comment''' ||
 …
 === Sechiba vs stomate (r6614) ===
 In ORCHIDEE trunk 4 the links between sechiba and stomate have been strengthened compared to previous ORCHIDEE trunks. As in previous versions, stomate makes use of variables calculated in sechiba but in ORCHIDEE trunk 4, sechiba requires information from stomate to work properly. It is possible to prescribe the canopy structure and thus only run sechiba. Set '''lai_map''' = y, the data for a canopy structure map need to come from an ORCHIDEE trunk 4 run with stomate. All the required information is stored in the sechiba restart file to enable restarting the model without stomate.
 === Tree ring width (r6721) ===
 Tree ring width is always calculated and is not controlled by any flags or additional parameters. The basal area increment is central in the allocation scheme when making use of the Deleuze and Dhote rule to account for within stand competition between trees with different dimensions. It is saved to the output variable CCDELTABA (mm2 day-1). Basal area increment can be used to calculate the tree ring width when assuming that the cross-section of a tree trunk is circular. The output variable CCTRW represents the radial increase of individual trees for each circumference class (mm day-1). Since CCTRW is simply sqrt(ba_later/pi) - sqrt(ba_beginning/pi), it reconstructs trees from zero at year 1 removing the effect of BA_init. An implication of this approach is that the value at the first time step does not only include the growth calculated in stomate_growth_fun_all but also the basal area that was prescribed in stomate_prescribe.f90. The contribution of the initial tree dimensions prescribed in stomate_prescribe becomes more important if bigger trees are prescribed. Both CCDELTABA and CCTRW are written to stomate_4dim.nc.
 === Vertical discretization soil carbon (r6721) ===
 To be completed.
 === Wind throw (r6614) ===
 The calculation of wind storm damage can be activated by setting '''ok_windthrow''' to y in the orchidee.def. This module calculates the critical wind speed of a stand taking stand and soil properties into account. If the stand is managed, the damaged trees are salvaged logged. If the stand is unmanaged the damaged  trees are left on-site to decompose. The default setting for ok_windthrow is n. The damaged fractions of the stands are replanted and moved to the first age class (if more than 1 age class is used).
+=== Sechiba vs stomate ===
+Describes r6614. In ORCHIDEE trunk 4 the links between sechiba and stomate have been strengthened compared to previous ORCHIDEE trunks. As in previous versions, stomate makes use of variables calculated in sechiba but in ORCHIDEE trunk 4, sechiba requires information from stomate to work properly. It is possible to prescribe the canopy structure and thus only run sechiba. Set '''lai_map''' = y, the data for a canopy structure map need to come from an ORCHIDEE trunk 4 run with stomate. All the required information is stored in the sechiba restart file to enable restarting the model without stomate.
+=== Tree ring width ===
+Describes r6721. Tree ring width is always calculated and is not controlled by any flags or additional parameters. The basal area increment is central in the allocation scheme when making use of the Deleuze and Dhote rule to account for within stand competition between trees with different dimensions. It is saved to the output variable CCDELTABA (mm2 day-1). Basal area increment can be used to calculate the tree ring width when assuming that the cross-section of a tree trunk is circular. The output variable CCTRW represents the radial increase of individual trees for each circumference class (mm day-1). Since CCTRW is simply sqrt(ba_later/pi) - sqrt(ba_beginning/pi), it reconstructs trees from zero at year 1 removing the effect of BA_init. An implication of this approach is that the value at the first time step does not only include the growth calculated in stomate_growth_fun_all but also the basal area that was prescribed in stomate_prescribe.f90. The contribution of the initial tree dimensions prescribed in stomate_prescribe becomes more important if bigger trees are prescribed. Both CCDELTABA and CCTRW are written to stomate_4dim.nc.
+=== Vertical discretization soil carbon ===
+Describes r6721. To be completed.
+=== Wind throw ===
+Describes r6614. The calculation of wind storm damage can be activated by setting '''ok_windthrow''' to y in the orchidee.def. This module calculates the critical wind speed of a stand taking stand and soil properties into account. If the stand is managed, the damaged trees are salvaged logged. If the stand is unmanaged the damaged  trees are left on-site to decompose. The default setting for ok_windthrow is n. The damaged fractions of the stands are replanted and moved to the first age class (if more than 1 age class is used).