Changes between Version 35 and Version 36 of Documentation/TrunkFunctionality4


Ignore:
Timestamp:
2020-04-10T10:48:54+02:00 (4 years ago)
Author:
luyssaert
Comment:

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  • Documentation/TrunkFunctionality4

    v35 v36  
    1515== Fair use policy == 
    1616Before downloading and using the trunk, please, read and adhere to the [https://forge.ipsl.jussieu.fr/orchidee/wiki/GroupActivities/UseOfORCHIDEEpolicy/InternalFair-use-policy '''FAIR USE POLICY''']. 
    17 The label '''restricted use''' implies that if you are interested in setting up a study that heavily relies on this functionality you are requested to contact the developers to discuss beforehand whether your intended use is in conflict with the ongoing work of the developer. If this functionality is not the core of your study, you are free to use it. For example, if you are planning to study global gpp you can use the water stress without any further concern, if you are planning to study the response of a specific PFT to droughts, your study heavily relies on the water stress and so you are requested to contact the developer. In case of doubt contact the ORCHIDEE team.  
     17The label '''restrictions apply''' implies that if you are interested in setting up a study that heavily relies on this functionality you are requested to contact the developers to discuss beforehand whether your intended use is in conflict with the ongoing work of the developer. If this functionality is not the core of your study, you are free to use it. For example, if you are planning to study global gpp you can use the water stress without any further concern, if you are planning to study the response of a specific PFT to droughts, your study heavily relies on the water stress and so you are requested to contact the developer. In case of doubt contact the ORCHIDEE team.  
    1818 
    1919 
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    112112 
    113113 
    114 === Bark beetles ('''restricted use'''; r6614) === 
     114=== Bark beetles ('''restrictions apply'''; r6614) === 
    115115The 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. 
    116116 
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    229229 
    230230 
    231 === Litter raking ('''restricted use'''; r6614) === 
     231=== Litter raking ('''restrictions apply'''; r6614) === 
    232232Tree 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 
    233233 
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    240240ORCHIDEE trunk 4 calculates the number of individuals and uses this as a criterion to initiate a stand replacing disturbance. This approach, guided by the self-thinning relationship, avoids the need for a stand-level turnover time. ORCHIDEE-CN, and ORCHIDEE-CNP still make use of stand-level turnover. Note that the meaning of residence_time is very different between the CAN branch and the trunk.  In the trunk biomass has no age and thus the residence time accounts for all forest dynamics including self-thinning, pests, diseases and windthrow. In the CAN branch, biomass does have an age and self-thinning is explicitly accounted for, hence, the residence time should be much higher as it only accounts for pest, diseases and windthrow. Even the latter is not exact because as long as those disturbances are small scale they are probably accounted for in the parametrization of self-thinning. 
    241241 
    242 === Nitrogen cycle ('''restricted use'''; r6614) === 
     242=== Nitrogen cycle ('''restrictions apply'''; r6614) === 
    243243ORCHIDEE 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. 
    244244 
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    292292 
    293293 
    294 === Plant water stress ('''restricted use'''; r6614) === 
     294=== Plant water stress ('''restrictions apply'''; r6614) === 
    295295With ORCHIDEE trunk 4 there are two option to calculate waters stress: 
    296296* 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. 
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    315315 
    316316 
    317 === Recruitment ('''restricted use'''; r6614) === 
     317=== Recruitment ('''restrictions apply'''; r6614) === 
    318318When 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. 
    319319 
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    323323 
    324324 
    325 === River routing (r6614) === 
     325=== River routing ('''restrictions apply'''; r6614) === 
    326326This 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. 
    327327 
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    346346 
    347347 
    348 === Single layer vs multi layer energy budget ('''restricted use'''; r6614) === 
     348=== Single layer vs multi layer energy budget ('''restrictions apply'''; r6614) === 
    349349There 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: 
    350350A - Use the energy scheme as found in the original enerbil.f90 
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    355355Energy_control has 5 possible settings: 
    356356* Single layer, using the multi layer energy scheme (i.e. choice B above) 
    357 * Multi-layer energy budget ('''restricted use''') 
     357* Multi-layer energy budget ('''restrictions apply''') 
    358358* User specific as set in the run.def 
    359359* Single layer, using the original enerbil scheme (i.e. choice A above) 
    … …  
    3623622 - option to use enerbil module and original water stress (not hydraulic architecture). 
    3633633 - The energy budget is calculated using the multi-layer energy scheme with a single layer: ok_hydrol_arch, ok_gs_feedback, ok_impose_canopy_structure and ok_mleb all TRUE, but The energy budget is only calculated for a single layer (jnlvls is 1,jnlvls_under is 0,jnlvls_canopy is 1,jnlvls_over is 0). No mleb output, ok_mleb_history_file is set to FALSE. 
    364 4 - multi-layer energy budget ('''restricted use'''): ok_hydrol_arch, ok_gs_feedback and ok_mleb all TRUE. ok_impose_canopy_structure is False, and the energy budget is calculated for multiple layers (jnlvls is 29,jnlvls_under is 10,jnlvls_canopy is 10,jnlvls_over is 9). No mleb output, ok_mleb_history_file is set to  FALSE. 
     3644 - multi-layer energy budget ('''restrictions apply'''): ok_hydrol_arch, ok_gs_feedback and ok_mleb all TRUE. ok_impose_canopy_structure is False, and the energy budget is calculated for multiple layers (jnlvls is 29,jnlvls_under is 10,jnlvls_canopy is 10,jnlvls_over is 9). No mleb output, ok_mleb_history_file is set to  FALSE. 
    3653655 - user specific: user specific settings for these controls and layers as defined in the run.def by the user. 
    366366 
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    413413In 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. 
    414414 
    415 === Tree ring width ('''restricted use'''; r6721) === 
     415=== Tree ring width ('''restrictions apply'''; r6721) === 
    416416To be completed. 
    417417 
    418 === Vertical discretization soil carbon ('''restricted use'''; r6721) === 
     418=== Vertical discretization soil carbon ('''restrictions apply'''; r6721) === 
    419419To be completed. 
    420420