Changes between Version 140 and Version 141 of DevelopmentActivities/ORCHIDEE-DOFOCO


Ignore:
Timestamp:
2017-06-22T15:40:15+02:00 (7 years ago)
Author:
luyssaert
Comment:

--

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  • DevelopmentActivities/ORCHIDEE-DOFOCO

    v140 v141  
    55 
    66Known conflicts with the trunk: tot_bare_soil, VIS/NIR snow albedo 
     7 
    78Missing functionalities compared to the trunk: DGVM, fire disturbances, and net land cover change 
     9 
    810Missing functionalities compared to ORCHIDEE-CAN (add these and we can close the branch): wind throw, land cover change, and species change 
    9 Better functionalities than those available in the trunk, ORCHIDEE-CN or ORCHIDEE-CN-CAN: spitfire for fire disturbanmces and gross land cover changes. 
     11 
     12Better functionalities than those available in the trunk, ORCHIDEE-CN or ORCHIDEE-CN-CAN: spitfire for fire disturbances and gross land cover changes. 
    1013 
    1114Coupling: Trunk has been extensively tested, ORCHIDEE-CN? ORCHIDEE-CAN has been used nudged and zoomed. Several key parameters have changed: albedo, roughness is now dynamic, more landscape heterogeneity when using age classes.  
    … …  
    2326Add instructions 
    2427 
    25 == Some explanations about the (new) parameters == 
    26 === stomate === 
    27 ORCHIDEE-CN-CAN strengthen the links between sechiba and stomate. As in previous versions, stomate makes use of variables calculated in sechiba but in ORCHIDEE-CAN and ORCHIDEE-CN-CAN, sechiba requires information from stomate to work properly. For the moment set '''stomate_ok_stomate''' to y (_AUTOBLOCKER_). For the future it seems possible to prescribe LAI and assume a canopy structure but this code still needs to be restored and tested. For the time being set '''lai_map''' = n. 
     28== Parameter settings (alphabetical order) == 
     29=== Age classes === 
     30Age 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. Age classes are independent of the number of diameter classes. Using age classes adds a lot of details in 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 a low albedo, a high roughness, ... 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, ...  
     31 
     32Age classes were defined as separate PFTs and if wanted different age classes of the same PFT could be 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 but for each PFT it can be decided whether age classes are used or not. This adds a lot of flexibility to the model. ORCHIDEE-CAN, 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 setting-up the run.def. A python-script was written to create this kind of run.def. Increasing the number of PFTs has important consequences for the speed of the model and the memory use. 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. 
     33 
     34The number of age classes is defined by the parameter '''NAGEC'''. Setting this parameter to 1 is a good start unless you have a special interest in using age classes. When NAGEC is set to more than 1, '''PFT_TO_MTC'''', '''AGEC_GROUP''' and '''PFT_NAME''' will all need to be carefully defined. See the attached run.def for a functional example. See below for some principles: 
     35NAGEC = 4 
     36Assume we want to use four age classes for all forests. We will end-up with 37 PFTs, the 1 for bare soil, C3 grass, C4 grass, C3 crop and C4 crop and 4 times 8 for the 8 forest PFTs. Thus NVM = 37 
     37 
     38Because we still use the 13 default MTC we can use the default maps. Let the model know how many MTCs it should find on the maps: 
     39NVMAP=13 
     40 
     41If you want to use IMPOSE_VEG=y then only vegetation should be added to the youngest age class. ORCHIDEE will update the vegetation fractions during the simulations 
     42{{{ 
     43SECHIBA_VEG_01=0.0769230769231 
     44SECHIBA_VEG_02=0.0769230769231 
     45SECHIBA_VEG_03=0.0 
     46SECHIBA_VEG_04=0.0 
     47SECHIBA_VEG_05=0.0 
     48... 
     49 
     50SECHIBA_VEGMAX_01=0.0769230769231 
     51SECHIBA_VEGMAX_02=0.0769230769231 
     52SECHIBA_VEGMAX_03=0.0 
     53SECHIBA_VEGMAX_04=0.0 
     54SECHIBA_VEGMAX_05=0.0 
     55... 
     56}}} 
     57Link PFTs to MTCs  
     58{{{ 
     59PFT_TO_MTC_01=1 
     60PFT_TO_MTC_02=2 
     61PFT_TO_MTC_03=2 
     62PFT_TO_MTC_04=2 
     63PFT_TO_MTC_05=2 
     64... 
     65}}} 
     66 
     67Tell ORCHIDEE which PFTs have a successional relationship 
     68{{{ 
     69AGEC_GROUP_01=1 
     70AGEC_GROUP_02=2 
     71AGEC_GROUP_03=2 
     72AGEC_GROUP_04=2 
     73AGEC_GROUP_05=2 
     74... 
     75}}} 
     76 
     77Give all PFTs a name for clarity 
     78{{{ 
     79PFT_NAME__01=Soilbare 
     80PFT_NAME__02=Broadleavedevergreentropical_age01 
     81PFT_NAME__03=Broadleavedevergreentropical_age02 
     82PFT_NAME__04=Broadleavedevergreentropical_age03 
     83PFT_NAME__05=Broadleavedevergreentropical_age04 
     84... 
     85}}} 
     86 
     87=== Albedo === 
     88ORCHIDEE-CN-CAN makes use of a two stream radiative transfer scheme through the canopy. 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). In ORCHIDEE-CN-CAN the same scheme is used to simulate the reflected, transmitted and absorbed light. 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-CN-CAN cannot revert to previous approaches for calculating albedo. 
     89  
     90The 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 VIS and NIR 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. 
    2891 
    2992=== Allocation === 
    … …  
    3598 
    3699MENTION K_LATOSA, CONDUCTIVITIES, SLA, RESPIRATION_COEFF, ... TAU_SAP, TAU_WOOD, ... 
    37   
     100 
     101=== Background albedo === 
     102If covered by snow, the background albedo is calculated by the snow module and accounts for snow age and snow density (needs to be checked – last time snow did not account for NIR). If not covered by snow the background albedo is not simulated but prescribed by the parameters '''bgrd_ref_vis''' and '''bgrd_ref_nir'''. 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-CN-CAN has two options to prescribe the background albedo: 
     103 
     1041 - The background albedo is prescribed per PFT but is constant throughout the year. This is the option that has been used in ORCHIDEE-CAN and is the option that has been validated over Europe. Set '''alb_bg_modis''' = n. 
     105 
     1062 - The background albedo varies with time but 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 validated yet. Set '''alb_bg_modis''' = y. 
     107 
     108=== Coming soon === 
     1091 - Land cover change has been coded for age classes in ORCHIDEE-CAN. This code still needs to be merged into ORCHIDEE-CN-CAN. For the moment set '''land_cover_change''' = n and '''veget_update''' = 0Y. 
     110 
     1112 - Following a disturbance, tree species changes and forest management change can be prescribed or read from a map in ORCHIDEE-CAN. This code still needs to be merged into ORCHIDEE-CN-CAN. For the moment set '''lchange_species''' = n, '''read_species_change_map''' = n, and '''read_desired_fm_map''' = n 
     112 
     113=== Consistency checks === 
     114The code distinguishes between three options to check for mass balance problems. 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-CN-CAN will also check for the preservation of veget_max. 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. 
     115 
     1161 - 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 mass balance error is only written to the history file. No information is provided in which subroutine the problem occurred. 
     117 
     1182 - 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. 
     119 
     1203 - arr_act = 3 is recommended when having a problem with mass balance closure. The mass balance is explicitly checked in stomate.f90, stomate_lpj.f90 and all its subroutines. If a mass balance occurs, the model is stopped. 
     121 
     122=== CWRR vs Choinel === 
     123ORCHIDEE-CN-CAN was developed and tested with CWRR. Set '''hydrol_cwrr''' to y. The Choinel code is still available. The hydrological schemes were not touched during the development of ORCHIDEE-CN-CAN. 
     124 
    38125=== Diameter classes === 
    39126Diameter 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.  
    … …  
    49136The above declaration implies that 9/13th of the trees will always be in the smallest diameter class, 3/13th will be in the medium class and 1 tree out of 13 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.  
    50137 
    51 === Age classes === 
    52 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. Age classes are independent of the number of diameter classes. Using age classes adds a lot of details in 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 a low albedo, a high roughness, ... 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, ...  
    53  
    54 Age classes were defined as separate PFTs and if wanted different age classes of the same PFT could be 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 but for each PFT it can be decided whether age classes are used or not. This adds a lot of flexibility to the model. ORCHIDEE-CAN, 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 setting-up the run.def. A python-script was written to create this kind of run.def. Increasing the number of PFTs has important consequences for the speed of the model and the memory use. 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. 
    55  
    56 The number of age classes is defined by the parameter '''NAGEC'''. Setting this parameter to 1 is a good start unless you have a special interest in using age classes. When NAGEC is set to more than 1, '''PFT_TO_MTC'''', '''AGEC_GROUP''' and '''PFT_NAME''' will all need to be carefully defined. See the attached run.def for a functional example. See below for some principles: 
    57 NAGEC = 4 
    58 Assume we want to use four age classes for all forests. We will end-up with 37 PFTs, the 1 for bare soil, C3 grass, C4 grass, C3 crop and C4 crop and 4 times 8 for the 8 forest PFTs. Thus NVM = 37 
    59  
    60 Because we still use the 13 default MTC we can use the default maps. Let the model know how many MTCs it should find on the maps: 
    61 NVMAP=13 
    62  
    63 If you want to use IMPOSE_VEG=y then only vegetation should be added to the youngest age class. ORCHIDEE will update the vegetation fractions during the simulations 
    64 {{{ 
    65 SECHIBA_VEG_01=0.0769230769231 
    66 SECHIBA_VEG_02=0.0769230769231 
    67 SECHIBA_VEG_03=0.0 
    68 SECHIBA_VEG_04=0.0 
    69 SECHIBA_VEG_05=0.0 
    70 ... 
    71  
    72 SECHIBA_VEGMAX_01=0.0769230769231 
    73 SECHIBA_VEGMAX_02=0.0769230769231 
    74 SECHIBA_VEGMAX_03=0.0 
    75 SECHIBA_VEGMAX_04=0.0 
    76 SECHIBA_VEGMAX_05=0.0 
    77 ... 
    78 }}} 
    79 Link PFTs to MTCs  
    80 {{{ 
    81 PFT_TO_MTC_01=1 
    82 PFT_TO_MTC_02=2 
    83 PFT_TO_MTC_03=2 
    84 PFT_TO_MTC_04=2 
    85 PFT_TO_MTC_05=2 
    86 ... 
    87 }}} 
    88  
    89 Tell ORCHIDEE which PFTs have a successional relationship 
    90 {{{ 
    91 AGEC_GROUP_01=1 
    92 AGEC_GROUP_02=2 
    93 AGEC_GROUP_03=2 
    94 AGEC_GROUP_04=2 
    95 AGEC_GROUP_05=2 
    96 ... 
    97 }}} 
    98  
    99 Give all PFTs a name for clarity 
    100 {{{ 
    101 PFT_NAME__01=Soilbare 
    102 PFT_NAME__02=Broadleavedevergreentropical_age01 
    103 PFT_NAME__03=Broadleavedevergreentropical_age02 
    104 PFT_NAME__04=Broadleavedevergreentropical_age03 
    105 PFT_NAME__05=Broadleavedevergreentropical_age04 
    106 ... 
    107 }}} 
    108  
    109 === CWRR vs Choinel === 
    110 ORCHIDEE-CN-CAN was developed and tested with CWRR. Set '''hydrol_cwrr''' to y. The Choinel code is still available. The hydrological schemes were not touched during the development of ORCHIDEE-CN-CAN. 
     138=== Forest management === 
     13970% of the global forest are managed invalidating 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, i.e., Deleuze and Dhote and RDI based management were retained. If the forest management strategy is not specified the default value "unmanaged" (FM = 1) is used. This implies that there are no thinning or harvest. Once the stand density drops below the threshold or the tree diameter exceeds another threshold a stand replacing disturbance is applied and a new stand is prescribed in the next time step. Therefore, the biomass pools in ORCHIDEE-CN-CAN no longer depend on a prescribed longevity. 
     140 
     141When developing and testing the model, a single forest management strategy can be applied for all pixels and PFTs. ORCHIDEE-CN-CAN distinguishes 4 different strategies: 
     142 
     1431 – FM=1 unmanaged 
     144 
     1452 – FM=2 high stand management: with RDI based thinnings and density/diameter based final harvest 
     146 
     1473 – FM=3 coppice 
     148 
     1494 – FM=4 short rotation coppice with willow or poplar 
     150 
     151Set '''read_fm_map''' to n and specify the desired management strategy (1-4) through '''forest_managed_forced'''. 
     152 
     153For applications that focus on forestry or require landscape heterogeneity, a PFT-specific management strategy can be read from a spatially explicit map. Thus, the same PFT in different pixels can be assigned a different management strategy. However, within a pixel a single PFT can only have one management strategy. Unless, one wants to run forest management over Europe the user will have to create his/her forest management maps first. Set '''read_fm_map''' to y and specify the location of the forest management map in COMP/stomate.card. Check the existing forest management maps for Europe for an example of how the map should be defined. 
     154 
     155When prescribing a forest stand (independent of forest management) the Initial density '''nmaxtrees''', and the range of the initial tree height of the seedlings needs to be specified '''height_init_min''' and '''height_init_max'''. Irrespective of the management strategy the maximum carrying capacity needs to be described. Carrying capacity was formalized through the self-thinning relationship which makes use of two parameters '''alpha_self_thinning''' and '''beta_self_thinning'''. As a fail-safe option the longevity of a stand is still defined but should only be used when all other criteria fail to kill the stand (not observed). Longevity is defined by the parameter '''residence_time'''. 
     156 
     157The details of each of the 4 management strategies can be refined through a set of PFT-specific parameters. Note that not every management strategy makes use of all parameters. For more details see the SI of Naudts et al 2015 (last table).  The different management strategies require parameter values for : first thinning height '''h_first''', stand replacing density '''ntrees_dia_profit''', harvest diameter '''max_harvest_dia''', ccppice diameter '''coppice_diameter''', rotation length '''src_rot_length''', number of rotations '''src_nrots''', fuelwood diameter '''fuelwood_diameter''' and the minimum and maximum alpha and beta (thus 4 parameters) specifying the RDI range '''alpha_rdi_upper''', '''alpha_rdi_lower''', '''beta_rdi_upper''' and '''beta_rdi_lower'''. 
     158 
     159According to economic theory, high-stand forest are harvested when the actual growth drops below the long-term growth. This has been implemented in ORCHIDEE-CAN and ORCHIDEE-CN-CAN. This feature was found to be very sensitive to the time frame for which actual increment was calculated. This option can be by-passed by setting this period unrealistically high, for example, '''n_pai''' =1000. Persons interested in further testing/developing this feature should set this parameter (unit: years) to 5 or 10. 
     160 
     161While developing the code some conflicts were encountered between RDI and self-thinning. As a first solution an additional threshold was introduced '''rdi_limit_upper'''. When debugging progressed this threshold was set to 0.99 (if set to 1.00 there is no correction any more). The initial problem was resolved but the initial fix has not been removed yet. For the time being set rdi_limit_upper to 0.99. 
     162 
     163CHECK: MAX_HARVEST_DIA 
     164 
     165=== Litter raking === 
     166USE_LITTER_RAKING=n 
     167 
     168=== Nitrogen cycle === 
     169ORCHIDEE-CN-CAN strictly follows ORCHIDEE-CN 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. The parameter '''ímpose_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 imnpose_cn = n. With this setting the N-cycle is closed (checked when checking for mass balance closure) it will require a spin-up to produce reasonale results. 
     170 
     171=== Plant water stress === 
     172MENTION 2 OPTIONS 
     173MENTION conductivities and cavitation 
     174 
     175=== Recruitment === 
     176When 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. 
     177 
     178ORCHIDEE-CN-CAN can simulate recruitment for each PFT separatly by setting '''recruitment_pft_xx''' 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_xx was introduced. If the '''recruitment''' flag is set to true, the settings of recruitment_pft_xx will be used. If the '''recruitment''' flag is set to false, the settings of recruitment_pft_xx will be ignored and the model runs without recruitment. 
     179 
     180Recruitment has been developed, tested and validated for tropical forests. There is no reason why it shouldn't work for other forests but that needs to be confirmed. At present recruitment was introduced at the PFT level. It probably makes more sense to link it to the management strategy than to the PFT. This needs to be checked. 
    111181 
    112182=== River routing === 
    113183The river routing code was not touched during the development of ORCHIDEE-CN-CAN. This functionality has not been tested yet for ORCHIDEE-CN-CAN. Unless rivers are your main interest, set '''river_routing''' to n.  
    114184 
    115 === Albedo === 
    116 ORCHIDEE-CN-CAN makes use of a two stream radiative transfer scheme through the canopy. 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). In ORCHIDEE-CN-CAN the same scheme is used to simulate the reflected, transmitted and absorbed light. 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-CN-CAN cannot revert to previous approaches for calculating albedo. 
    117   
    118 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 VIS and NIR 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. 
    119  
    120 === Background albedo === 
    121 If covered by snow, the background albedo is calculated by the snow module and accounts for snow age and snow density (needs to be checked – last time snow did not account for NIR). If not covered by snow the background albedo is not simulated but prescribed by the parameters '''bgrd_ref_vis''' and '''bgrd_ref_nir'''. 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-CN-CAN has two options to prescribe the background albedo: 
    122  
    123 1 - The background albedo is prescribed per PFT but is constant throughout the year. This is the option that has been used in ORCHIDEE-CAN and is the option that has been validated over Europe. Set '''alb_bg_modis''' = n. 
    124  
    125 2 - The background albedo varies with time but 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 validated yet. Set '''alb_bg_modis''' = y. 
    126  
    127185=== Single layer vs multi layer energy budget === 
    128  
    129 The 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. This can, however, be done by two different methods that gives the exact same results: 
     186There 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. This can, however, be done by two different methods that gives the exact same results: 
    130187 
    131188A: use the energy scheme as found in the original enerbil.f90 
    … …  
    193250}}} 
    194251 
    195 === Plant water stress === 
    196 MENTION 2 OPTIONS 
    197 MENTION conductivities and cavitation 
    198  
    199252=== Specific leaf area === 
    200253Similar to ORCHIDEE-CN, ORCHIDEE-CN-CAN 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. The current implementation of dynamic SLA is basic and there is room to enhance consistency in the calculations, for example, by recalculation the allocation factors KF and LF as a function of SLA. 
    201254 
    202 === Forest management === 
    203 70% of the global forest are managed invalidating 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, i.e., Deleuze and Dhote and RDI based management were retained. If the forest management strategy is not specified the default value "unmanaged" (FM = 1) is used. This implies that there are no thinning or harvest. Once the stand density drops below the threshold or the tree diameter exceeds another threshold a stand replacing disturbance is applied and a new stand is prescribed in the next time step. Therefore, the biomass pools in ORCHIDEE-CN-CAN no longer depend on a prescribed longevity. 
    204  
    205 When developing and testing the model, a single forest management strategy can be applied for all pixels and PFTs. ORCHIDEE-CN-CAN distinguishes 4 different strategies: 
    206  
    207 1 – FM=1 unmanaged 
    208  
    209 2 – FM=2 high stand management: with RDI based thinnings and density/diameter based final harvest 
    210  
    211 3 – FM=3 coppice 
    212  
    213 4 – FM=4 short rotation coppice with willow or poplar 
    214  
    215 Set '''read_fm_map''' to n and specify the desired management strategy (1-4) through '''forest_managed_forced'''. 
    216  
    217 For applications that focus on forestry or require landscape heterogeneity, a PFT-specific management strategy can be read from a spatially explicit map. Thus, the same PFT in different pixels can be assigned a different management strategy. However, within a pixel a single PFT can only have one management strategy. Unless, one wants to run forest management over Europe the user will have to create his/her forest management maps first. Set '''read_fm_map''' to y and specify the location of the forest management map in COMP/stomate.card. Check the existing forest management maps for Europe for an example of how the map should be defined. 
    218  
    219 When prescribing a forest stand (independent of forest management) the Initial density '''nmaxtrees''', and the range of the initial tree height of the seedlings needs to be specified '''height_init_min''' and '''height_init_max'''. Irrespective of the management strategy the maximum carrying capacity needs to be described. Carrying capacity was formalized through the self-thinning relationship which makes use of two parameters '''alpha_self_thinning''' and '''beta_self_thinning'''. As a fail-safe option the longevity of a stand is still defined but should only be used when all other criteria fail to kill the stand (not observed). Longevity is defined by the parameter '''residence_time'''. 
    220  
    221 The details of each of the 4 management strategies can be refined through a set of PFT-specific parameters. Note that not every management strategy makes use of all parameters. For more details see the SI of Naudts et al 2015 (last table).  The different management strategies require parameter values for : first thinning height '''h_first''', stand replacing density '''ntrees_dia_profit''', harvest diameter '''max_harvest_dia''', ccppice diameter '''coppice_diameter''', rotation length '''src_rot_length''', number of rotations '''src_nrots''', fuelwood diameter '''fuelwood_diameter''' and the minimum and maximum alpha and beta (thus 4 parameters) specifying the RDI range '''alpha_rdi_upper''', '''alpha_rdi_lower''', '''beta_rdi_upper''' and '''beta_rdi_lower'''. 
    222  
    223 According to economic theory, high-stand forest are harvested when the actual growth drops below the long-term growth. This has been implemented in ORCHIDEE-CAN and ORCHIDEE-CN-CAN. This feature was found to be very sensitive to the time frame for which actual increment was calculated. This option can be by-passed by setting this period unrealistically high, for example, '''n_pai''' =1000. Persons interested in further testing/developing this feature should set this parameter (unit: years) to 5 or 10. 
    224  
    225 While developing the code some conflicts were encountered between RDI and self-thinning. As a first solution an additional threshold was introduced '''rdi_limit_upper'''. When debugging progressed this threshold was set to 0.99 (if set to 1.00 there is no correction any more). The initial problem was resolved but the initial fix has not been removed yet. For the time being set rdi_limit_upper to 0.99. 
    226  
    227 CHECK: MAX_HARVEST_DIA 
    228  
    229  
    230 === Consistency checks === 
    231 The code distinguishes between three options to check for mass balance problems. 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-CN-CAN will also check for the preservation of veget_max. 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. 
    232  
    233 1 - 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 mass balance error is only written to the history file. No information is provided in which subroutine the problem occurred. 
    234  
    235 2 - 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. 
    236  
    237 3 - arr_act = 3 is recommended when having a problem with mass balance closure. The mass balance is explicitly checked in stomate.f90, stomate_lpj.f90 and all its subroutines. If a mass balance occurs, the model is stopped. 
    238  
    239 === Nitrogen cycle === 
    240 ORCHIDEE-CN-CAN strictly follows ORCHIDEE-CN 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. The parameter '''ímpose_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 imnpose_cn = n. With this setting the N-cycle is closed (checked when checking for mass balance closure) it will require a spin-up to produce reasonale results. 
    241  
    242 === Recruitment === 
    243 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. 
    244  
    245 ORCHIDEE-CN-CAN can simulate recruitment for each PFT separatly by setting '''recruitment_pft_xx''' 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_xx was introduced. If the '''recruitment''' flag is set to true, the settings of recruitment_pft_xx will be used. If the '''recruitment''' flag is set to false, the settings of recruitment_pft_xx will be ignored and the model runs without recruitment. 
    246  
    247 Recruitment has been developed, tested and validated for tropical forests. There is no reason why it shouldn't work for other forests but that needs to be confirmed. At present recruitment was introduced at the PFT level. It probably makes more sense to link it to the management strategy than to the PFT. This needs to be checked. 
    248  
    249 === Litter raking === 
    250 USE_LITTER_RAKING=n 
    251  
    252  
    253 === Comming soon === 
    254 1 - Land cover change has been coded for age classes in ORCHIDEE-CAN. This code still needs to be merged into ORCHIDEE-CN-CAN. For the moment set '''land_cover_change''' = n and '''veget_update''' = 0Y. 
    255  
    256 2 - Following a disturbance, tree species changes and forest management change can be prescribed or read from a map in ORCHIDEE-CAN. This code still needs to be merged into ORCHIDEE-CN-CAN. For the moment set '''lchange_species''' = n, '''read_species_change_map''' = n, and '''read_desired_fm_map''' = n  
     255=== stomate === 
     256ORCHIDEE-CN-CAN strengthen the links between sechiba and stomate. As in previous versions, stomate makes use of variables calculated in sechiba but in ORCHIDEE-CAN and ORCHIDEE-CN-CAN, sechiba requires information from stomate to work properly. For the moment set '''stomate_ok_stomate''' to y (_AUTOBLOCKER_). For the future it seems possible to prescribe LAI and assume a canopy structure but this code still needs to be restored and tested. For the time being set '''lai_map''' = n. 
     257