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Requirements
Requirement: name-of-requirement-here
Date last modified:
Contributors: (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-hereNew modules are added for new developments
Date last modified: 8/28/2015
Contributors:
Qing Qing Zhu
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.
- Two competition algorithms are implemented
- Soil microbes outcompete plants
UPmic = min(Nav, UPmic)
UPplant = min(max(Nav - UPmic,0), UPplant)
UPmic and UPplant are microbial decomposer and plant nutrient uptake rate. Nav is soil available nutrient pool size - Plant-microbe competition is scaled by their functional traits (e.g., biomass density) through ECA formulation
UPmic = VMAXmic * [Emic]*[Nav]/(KMmic + [Nav] + [Emic] + [Eplant]*KMmic/KMplant)
UPplant = VMAXplant * [Eplant]*[Nav]/(KMplant + [Nav] + [Eplant] + [Emic]*KMplant/KMmic)
VMAX and KM are kinetics parameters, Emic and Eplant are nutrient carrier enzyme abundance for decomposing microbes and plants - Leaf level physiology: how does N/P limitation on GPP occur
- VCMAX = f(leafN, leafP); JMAX = f(leafN, leafP)
- VCMAX and JMAX are maximum carboxylation and electron transport rate for photosynthesis. Their relationships with leaf level N/P concentration are derived form TRY database.
- N2 fixation = f(carbon cost of root nitrogen uptake, carbon cost of N2 fixation, plant phosphorus status)
- N2 fixation occur only when roots are not able to acquire enough nitrogen. N2 fixation rate could be limited plant phosphorus shortage.
- Phosphatase activity = f(nitrogen cost, plant nitrogen status, plant phosphorus status)
- Phosphatase activity is nitrogen expensive. It occur only when the benefit is larger than the cost.
Design and Implementation
Implementation:
short-desciption-of-implementation-hereOffline test with MATLAB codes plus online test within ACME
Date last modified:
108/
2028/2015
Contributors:
Gautam BishtQing Zhu
- Initial prototype of the VSFM model will be developed N-COM model has been developed and tested in MATLAB.
- The VSFM implementation in ACME would use PETSc.
- SNES solver of PETSc will be used to solve the system of nonlinear equations that is obtained after applying spatial and temporal discretization The future goal of ACME is to solve tightly coupled transport of water in the soil with other relevant physics (e.g. transport of water in roots [ACME V2]). Thus, the current VSFM will use DMComposite feature of PETSc. DMComposite allows an application to breaN-COM model is being integrated in ACME
Planned Verification and Unit Testing
Verification and Unit Testing:
short-desciption-of-testing-hereBenchmarking
Date last modified:
108/
2028/2015
Contributors: Gautam BishtQing Zhu
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?
ACME with N-COM codes will be evaluated using ILAMB benchmarking package.
Planned Validation Testing
Validation Testing:
short-desciption-of-testing-hereModel validate with global dataset
Date last modified:
108/
2028/2015
Contributors: Gautam BishtQing Zhu
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?
The VSFM]
ACME with N-COM codes, will be
tested against previously benchmark problems published.Additionally, VSFM will be tested against PFLOTRAN for certain benchmark problems.validated against global scale nitrogen/phosphorus fertilization experiments, across multiple ecosystems.
Planned Performance Testing
Performance Testing: short-
desciptiondescription-of-testing-here
Date last modified:8/28/2015
Contributors:
(add your name to this list if it does not appear)Qing Zhu
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?
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