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- Introduce a soil order-based parameterization of mortality in tropical forests
- Remove the second round of nutrient uptake for N and P
- Modification of plant N and C storage pool dynamics, and introduction of plant P storage pool dynamics
- Modification of subsurface drainage parameterization
- Improve efficiency of the previously introduced coupler bypass method for offline land simulation modethe parameterization of stress-deciduous phenology
Requirements
Requirement:
name-of-requirement-hereRepresent observed variation in tropical forest mortality
Date last modified:
// date
Contributors:
@ name (add your name to this list if it does not appear)Each requirement is to be listed under a ”section” heading, as there will be a one-to-one correspondence between requirements, design, proposed imple- mentation and testing. Requirements should not discuss technical software issues, but rather focus on model capability. To the extent possible, require- ments should be relatively independent of each other, thus allowing a clean design solution, implementation and testing plan.
Algorithmic Formulations
Design solution: short-description-of-proposed-solution-here
Date last modified:// date
Contributors: (add your name to this list if it does not appear)
For each requirement, there is a design solution that is intended to meet that requirement. Design solutions can include detailed technical discussions of PDEs, algorithms, solvers and similar, as well as technical discussion of performance issues. In general, this section should steer away from a detailed discussion of low-level software issues such as variable declarations, interfaces and sequencing.
Design and Implementation
Implementation: short-desciption-of-implementation-here
Date last modified: // date
Contributors: (add your name to this list if it does not appear)
This section should detail the plan for implementing the design solution for requirement XXX. In general, this section is software-centric with a focus on software implementation. Pseudo code is appropriate in this section. Links to actual source code are appropriate. Project management items, such as svn branches, timelines and staffing are also appropriate. How do we typeset pseudo code?
Xiaojuan Yang, Peter Thornton, Daniel Ricciuto
Field studies have shown that edaphic factors exert a strong influence on tree mortality in tropical forests, with lower mortality in highly weathered Oxisols, and higher mortality in younger soils.
Quesada, C. A. et al. Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate. Biogeosciences 9, 2203–2246 (2012)
Galbraith D, Malhi Y, Affum-Baffoe K, Castanho ADA, Doughty CE, et al. 2013. Residence times of woody biomass in tropical forests. Plant Ecol. Divers. 6:139–57
Requirement: Remove redundant implementation of nutrient uptake
Date last modified:
Contributors: Xiaojuan Yang, Peter Thornton, Daniel Ricciuto
The original implementation of the relative demand hypothesis for competition between multiple plant and microbial components for available mineral nutrient resources included a single reconciliation of plant and microbial demand. In a later modification of that approach, a redundant second round of nutrient uptake was added. This redundant uptake implementation should be removed.
Requirement: Revise the handling of plant non-structural storage pools, in correspondence with observations
Date last modified:
Contributors: Peter Thornton, Daniel Ricciuto, Xiaojuan Yang
Plant carbon uptake in excess of allocation to new growth is retained in a non-structural carbohydrate pool, which turns over on a specified time scale, based on experimental evidence from Metcalfe et al. (2017).
Metcalfe, D. B., D. Ricciuto, S. Palmroth, C. Campbell, V. Hurry, J. F. Mao, S. G. Keel, S. Linder, X. Y. Shi, T. Nsholm, K. E. A. Ohlsson, M. Blackburn, P. E. Thornton and R. Oren (2017). "Informing climate models with rapid chamber measurements of forest carbon uptake." Global Change Biology 23(5): 2130-2139.
Requirement: Improve subsurface drainage parameterization based on observations
Date last modified:
Contributors: Daniel Ricciuto, Peter Thornton
Recent model-data evaluation effort showed that an earlier parameterization of subsurface drainage, used in CLM4.0, is more appropriate than the parameterization in CLM4.5, which served as the branch point for ELMv1 (Duarte et al., 2017).
Duarte, H. F., B. M. Raczka, D. M. Ricciuto, J. C. Lin, C. D. Koven, P. E. Thornton, D. R. Bowling, C. T. Lai, K. J. Bible and J. R. Ehleringer (2017). "Evaluating the Community Land Model (CLM4.5) at a coniferous forest site in northwestern United States using flux and carbon-isotope measurements." Biogeosciences 14(18): 4315-4340.
Requirement: Improve representation of stress-deciduous phenology
Date last modified:
Contributors: Daniel Ricciuto
Recent model evaluation indicated improved performance of the stress-deciduous phenology model by introducing a critical rainfall threshold to trigger leaf-on (Dahlin et al. 2015).
Dahlin, K. M., R. A. Fisher and P. J. Lawrence (2015). "Environmental drivers of drought deciduous phenology in the Community Land Model." Biogeosciences 12(16): 5061-5074.
Algorithmic Formulations, and Design Implementation
Design Solution: Represent observed variation in tropical forest mortality
Date last modified:
Contributors: Xiaojuan Yang, Peter Thornton, Daniel Ricciuto
Modified CNGapMortalityMod.F90 to implement the requirement according to observed patterns of soil order and tree mortality.
Design Solution: Remove redundant implementation of nutrient uptake
Date last modified:
Contributors: Xiaojuan Yang, Peter Thornton, Daniel Ricciuto
Modified CNAllocationMod.F90 to remove the second-pass nutrient uptake for N and P, restoring the intended design implementation.
Design Solution: Revise the handling of plant non-structural storage pools, in correspondence with observations
Date last modified:
Contributors: Peter Thornton, Daniel Ricciuto, Xiaojuan Yang
Modified the following files: src/biogeochem: CNAllocationMod.F90, CNMRespMod.F90 [C,N,P]StateUpdate[1,2,3].F90, CNGapMortalityMod.F90, CNFireMod.F90, [Carbon,Nirogen,Phosphorus]FluxType.F90
src/dyn_subgrid: dynConsBiogeochemMod.F90, dynHarvestMod.F90
main/pftvarcon.f90
Implemented the C storage pool dynamics described in the requirement. updated the N and P storage pool implementations to account for disturbance and mortality effects.
Design Solution: Improve subsurface drainage parameterization based on observations
Date last modified:
Contributors: Daniel Ricciuto, Peter Thornton
Modified the following files: biogeophys/SoilHydrologyMod.F90, and main/pftvarcon.f90.
Reverted the code to the CLM 4.0 implementation.
Design Solution: Improve representation of stress-deciduous phenology
Date last modified:
Contributors: Daniel Ricciuto
Modified the following files: biogeophys/SoilHydrologyMod.F90, and main/pftvarcon.f90.
Added the necessary dependence on critical rainfall threshold for leaf-on.
Planned Verification and Unit Testing
Verification and Unit Testing:
short-desciption-of-testing-hereExpert review
Date last modified:
Contributors:
(add your name to this list if it does not appear)How will XXX be tested? i.e. how will be we know when we have met requirement XXX. Will these unit tests be included in the ongoing going forward?
Peter Thornton, Daniel Ricciuto, Xiaojuan Yang
The named experts provided extensive review of each other's work, to verify that the design and implementations met the stated requirements. Model testing at each stage of implementation was used to verify that intended changes were correctly implemented, and that unintended changes were avoided.
Planned Validation Testing
Validation Testing:
short-desciption-of-testing-hereEvaluation with ILAMB and additional model-data metrics
Date last modified:
Contributors:
(add your name to this list if it does not appear)How will XXX be tested? What observational or other dataset will be used? i.e. how will be we know when we have met requirement XXX. Will these unit tests be included in the ongoing going forward?
Peter Thornton, Daniel Ricciuto, Xiaojuan Yang
The package of changes described here is being evaluated in a large set of offline simulations, with comparison against numerous observational constraints in the ILAMB framework, as part of the ongoing Land-BGC Intercomparison process. That process includes additional metrics, beyond ILAMB, which are so far not known to the model developers.
Planned Performance Testing
Performance Testing:
short-desciption-of-testing-hereOffline simulations on multiple platforms
How will XXX be tested? i.e. how will be we know when we have met requirement XXX. Will these unit tests be included in the ongoing going forward?
Date last modified:
Contributors:
(add your name to this list if it does not appear)Daniel Ricciuto
Many performance simulations have already been performed, in tests leading up to the Land-BGC simulations, and for the set of global offline simulations themselves.