The Design Document page provides a description of the algorithms, implementation and planned testing including unit, verification, validation and performance testing.
Design Document
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The first table in Design Document gives overview of this document, from this info the Design Documents Overview page is automatically created. In the table below, 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation
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In the table below, 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation, 
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Title: Nutrient COMpetition (N-COM): a mechanistic treatment of plant-soil nutrient interactions
Requirements and Design
ACME Land Group
Date: 8/28/2015
Summary
The ECA kinetics (Tang and Riley 2013; 2015) is being integrated into the ACME Land Model v1 (ALMv1) to represent multiple nutrient (i.e., nitrogen and phosphorus in v1) interactions and competition between multiple consumers (microbes, abiotic surfaces, and plants). This work has followed the original proposed tasks, primarily under M3.10 and M3.14. The code is being integrated in such a way as to allow for straightforward testing of different competition hypotheses.
References for this document:
- Ghimire, B., W. J. Riley, and C. D. Koven (2016), Representing leaf and root physiology in CLM results in improved global carbon and nitrogen cycling predictions, DOI: 10.1002/2015MS000538, JAMES.
- Tang, J. Y., and W. J. Riley (2015), Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions, Nature Climate Change, 5,WOS:00034651390001956-60.
- Zhu, Q., and W. J. Riley (2015), Improved modeling of soil nitrogen losses, Nature Climate Change, 5, doi:10.1038/nclimate2696, 705-706.
- Zhu, Q., W. J. Riley, J. Y. Tang, and C. D. Koven (2016), Multiple soil nutrient competition between plants, microbes, and mineral surfaces: Model development, parameterization, and example applications in several tropical forests, Biogeosciences, 13, 341-363.
- Tang, J. Y., and W. J. Riley (2013), A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition, Biogeosciences, 10,WOS:000329054600033, Doi 10.5194/Bg-10-8329-2013, 8329-8351.
Requirements
Requirement: Implement ECA kinetics to represent coupled N and P controls on carbon cycle processes
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
Implementing ECA kinetics to represent coupled N and P controls on carbon cycle processes requires the following code developments:
(1) Add nutrient competition through ECA kinetics: root, decomposing microbes, nitrate compete for NH4; root, decomposing microbes, denitrifier compete for NO3; root, decomposing microbes compete for POx
(2) Add root nutrient uptake kinetics to facilitate ECA kinetics implementation
(3)
Predict the nutrient uptake profile based on ECA kinetics
(4)
Link photosynthesis capacity with leaf nitrogen and phosphorus levels to facilitate ECA kinetics implementation
(5) Impelement dynamic allocation scheme considering nutrient, water, and light resource supplies
(6) Modify N2 fixation, mechanistically implement N2 fixation and its interaction with nitrogen
and phosphorus availability to allow ECA kinetics framework to uniformly treat competition
(
7) Mechanistically implement phosphatase activity and its interaction with nitrogen
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. and phosphorus availability in the ECA kinetics framework
Algorithmic Formulations
Design solution:
short-description-of-proposed-solution-hereNew modules are added to facilitate ECA kinetics and multi-nutrient competition
Date last modified:
8/28/2015Contributors:
QingQing 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.
William Riley (Unlicensed)
Two competition algorithms are implemented (Zhu et al. 2015, 2016):
- 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
- 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
The ECA kinetics integration requires:
- Leaf level physiology: how does N/P limitation on GPP occurN (Ghimire et al. 2016) and P leaf levels affect GPP
- 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 the TRY database.
- N2 fixation = f(carbon cost of root nitrogen uptake, carbon cost of N2 fixation, plant phosphorus status)
- N2 fixation occur occurs only when roots are not able to acquire enough nitrogen. N2 fixation rate could be limited by 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 Land Model (ALM)
Date last modified:
10/20/2015
Contributors:
Gautam Bisht
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?
- Initial prototype of the VSFM model will be developed 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 brea
Qing Zhu, William Riley (Unlicensed)
- Initial prototype of the N-COM model has been developed, tested, and published (Zhu et al. 2015, 2016).
- The N-COM model is being integrated in ACME following the Algorithmic Formulations described above.
Planned Verification and Unit Testing
Verification and Unit Testing:
short-desciption-of-testing-hereBenchmarking
10/20/2015Date last modified:
Contributors:
Gautam BishtQing Zhu, William Riley (Unlicensed)
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?
Once integrated with Master, we will perform the offline simulations described below (Planned Validation Testing) as a first cut at Verification. Unit testing of model subcomponents will be designed and implemented over the 6 months following code freeze (Nov. 1, 2015)
Planned Validation Testing
Validation Testing:
short-desciption-of-testing-hereModel validate with global, regional, and site-level datasets
10/20/2015Date last modified:
Contributors:
Gautam BishtQing Zhu, William Riley (Unlicensed)
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 ECA representation of nutrient competition is being, and will continue to be, tested against site-level, regional syntheses, and global remote-sensed and meta-analyses products:
- ACME with N-COM integration have been (N components; Ghimire et al. 2016), and will be, evaluated and validated using the International Land Model Benchmarking (ILAMB) package.
- ACME with N-COM integration will be validated against global scale nitrogen and phosphorus fertilization experiments, across multiple ecosystems. We plan to integrate this meta-analysis into the ILAMB package.
Planned Performance Testing
Performance Testing: short-desciption-of-testing-here
Date last modified:
Contributors: Qing Zhu,
(add your name to this list if it does not appearWilliam Riley (Unlicensed)
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?
- The ACME Land Model N-COM code will be tested with historical 1850 simulations timing, and compared to baseline ALMv0 performance timing.
- Preliminary results indicate no decrease in computational performance with integration of N-COM, but substantial increase in model simulation quality compared to observations
- Computational performance will be evaluated for offline and coupled global simulations using the ACME timing tools.