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Title:
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Implement prognostic phosphorus cycle into ACME land model
Requirements and Design
ACME
...
Land Group
Date: 09/15/
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2015
Summary
The
purpose of this section is to summarize what capability is to be added to the ACME Ocean and Ice system through this design process. It should be clear what new code will do that the current code does not. Summarizing the primary challenges with respect to software design and implementation is also appropriate for this section. Finally, this statement should contain general statement with regard to what is “success.”
Requirements
Requirement: name-of-requirement-here
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?
Planned Verification and Unit Testing
Verification and Unit Testing: short-desciption-of-testing-here
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?
Planned Validation Testing
Validation Testing: short-desciption-of-testing-here
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?
Planned Performance Testing
Performance Testing: short-desciption-of-testing-here
Date last modified:importance of nutrient in regulating carbon(C)-climate feedbacks has been increasingly recognized. While ACME V0 includes prognostic nitrogen(N) cycle and C-N interactions, phosphorus(P), the most limiting nutrient in productive lowland tropical forests, has yet to be considered. Here we implement prognostic P cycle and C-N-P interactions into ACME land model. This implementation will lead to a more accurate representation of C-nutrient interactions in ACME.
References:
Yang, X., Thornton, P. E., Ricciuto, D. M., and Post, W. M.: The role of phosphorus dynamics in tropical forests – a modeling study using CLM-CNP, Biogeosciences, 11, 1667-1681, doi:10.5194/bg-11-1667-2014, 2014.
Yang, X., Post, W. M., Thornton, P. E., and Jain, A.: The distribution of soil phosphorus for global biogeochemical modeling, Biogeosciences, 10, 2525-2537, doi:10.5194/bg-10-2525-2013, 2013.
Requirements
Requirement: Implement prognostic phosphorus cycle
Date last modified: 09/15/2015
Contributors: @ Xiaojuan Yang
All the needed phosphorus state and flux variables are added. Both geochemical and biological phosphorus processes are represented.
Requirement: Represent C-N-P interactions
Date last modified: 09/15/2015
Contributors: @ Xiaojuan Yang
This includes (1) P limitation on carbon cycle processes (2) biochemical mineralization through phosphatase activity
Requirement: Resolve N limitation vs P limitation
Date last modified: 09/15/2015
Contributors: @ Xiaojuan Yang
With both N and P in the model, N limitation vs P limitation is resolved to represent overall nutrient constraint on carbon cycle processes
Requirement: Model initialization for various P pools
Date last modified: 09/15/2015
Contributors: @ Xiaojuan Yang
Phosphorus cycle operates on geological time scales, it is not reasonable to spinup the model for tens of millions of years for model initialization. Instead we initialize the slow P pools globally with P maps that was generated(Yang et al., 2013)
Algorithmic Formulations
Design solution: Implement prognostic phosphorus cycle
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
All algorithmic formulations can be found in section 2.1.3 and 2.1.4 in Yang et al. (2014)
Design solution: Represent C-N-P interactions
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
All algorithmic formulations can be found in section 2.1.3 and 2.1.4 in Yang et al. (2014)
Design solution: Resolve N limitation vs P limitation
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
All algorithmic formulations can be found in section 2.1.2 in Yang et al. (2014)
Design solution: Model initialization for various P pools
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
The initialization maps can be found in Yang et al.(2013)
Design and Implementation
Implementation: Implement prognostic phosphorus cycle
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
P state and flux data types have been added. P state update subroutines have been added. Representation of Vegetation, litter, and soil organic matter P dynamics have been added. Inorganic P dynamics have been added
The following subroutines have been modified/added to include phosphorus cycle
• models/lnd/clm/src/biogeochem/CNAllocationMod.F90
• models/lnd/clm/src/biogeochem/CNBalanceCheckMod.F90
• models/lnd/clm/src/biogeochem/CNDecompCascadeCNMod.F90
• models/lnd/clm/src/biogeochem/CNDecompCascadeConType.F90
• models/lnd/clm/src/biogeochem/CNDecompMod.F90
• models/lnd/clm/src/biogeochem/CNEcosystemDynMod.F90
• models/lnd/clm/src/biogeochem/CNGapMortalityMod.F90
• models/lnd/clm/src/biogeochem/CNPhenologyMod.F90
• models/lnd/clm/src/biogeochem/CNPrecisionControlMod.F90
• models/lnd/clm/src/biogeochem/CNSoilLittVertTranspMod.F90
• models/lnd/clm/src/biogeochem/CNStateType.F90
• models/lnd/clm/src/biogeochem/CNWoodProductsMod.F90
• models/lnd/clm/src/biogeochem/PDynamicsMod.F90
• models/lnd/clm/src/biogeochem/PStateUpdate1Mod.F90
• models/lnd/clm/src/biogeochem/PStateUpdate2Mod.F90
• models/lnd/clm/src/biogeochem/PStateUpdate3Mod.F90
• models/lnd/clm/src/biogeochem/PhosphorusFluxType.F90
• models/lnd/clm/src/biogeochem/PhosphorusStateType.F90
• models/lnd/clm/src/main/EcophysConType.F90
• models/lnd/clm/src/main/SoilorderConType.F90
• models/lnd/clm/src/main/clm_driver.F90
• models/lnd/clm/src/main/clm_initializeMod.F90
• models/lnd/clm/src/main/clm_varctl.F90
• models/lnd/clm/src/main/clm_varpar.F90
• models/lnd/clm/src/main/controlMod.F90
• models/lnd/clm/src/main/pftvarcon.F90
• models/lnd/clm/src/main/restFileMod.F90
• models/lnd/clm/src/main/soilorder_varcon.F90
Implementation: Represent C-N-P interactions
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
The following subroutines have been modified or added
models/lnd/clm/src/biogeochem/CNDecompMod.F90
models/lnd/clm/src/biogeochem/CNAllocationMod.F90
models/lnd/clm/src/biogeochem/PDynamicsMod.F90
Implementation: Resolve N limitation vs P limitation
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
Implementation: Model initialization for various P pools
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
This is done by modifying the restart file before normal spinup
Planned Verification and Unit Testing
Verification and Unit Testing: Implement prognostic phosphorus cycle
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
Various component of the model has been tested against observations. For example, P dynamics during decomposition has been evaluated against CIDET dataset. Representation of biochemical mineralization has been evaluated against multiple observations.
Planned Validation Testing
Validation Testing: Implement prognostic phosphorus cycle
Date last modified: 09/16/2015
Contributors: Xiaojuan Yang
Model simulated phosphorus pools and fluxes will be evaluated against available observations such as Hedley P database(Yang et al., 2011). Other site level evaluations will be using (1) fertilization experiment along Hawaii chronosequence (2) sites along a P availability gradient in the Amazon basin. ILAMB will be used for regional and global evaluations. Other remote sensing products will also be used.
Planned Performance Testing
Performance Testing: Implement prognostic phosphorus cycle
Date last modified: 09/16/2015
Contributors: (add your name to this list if it does not appear)
How Computation performance 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?