The Design Document page provides a description of the algorithms, implementation and planned testing including unit, verification, validation and performance testing.
Design Document
Overview table for the owner and an approver of this feature
1.Name | CNP model with root uptake kinetics, leaf level physiology, soil nutrient competition, N-P interactions through N2 fixation and phosphatase activity |
| 2.Owner | Qing Zhu,William Riley (Unlicensed) |
| 3.Created | 8/28/2015 |
| 4.Equ |  - competed |
| 5.Ver |  - in progress |
| 6.Perf | - in progress |
| 7.Val | - in progress |
| 8.Approver | |
| 9.Approved Date |
Title: Nutrient COMpetition (N-COM): a mechanistic treatment of plant-soil nutrient interactions
Requirements and Design
ACME Land Group
Date: 8/28/2015
Summary
(1) Add nutrient competition: 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
(3) Modify the nutrient uptake profile
(4) Link leaf phosphorus level with photosynthesis capacity
(5) Modify N2 fixation, mechanistically implement N2 fixation and its interaction with nitrogen/phosphorus availability
(6) Phosphatase activities, mechanistically implement phosphatase activity and its interaction with nitrogen/phosphorus availability
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: New modules are added for new developments
Date last modified: 8/28/2015
Contributors: Qing Zhu
- 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: Offline test with MATLAB codes plus online test within ACME
Date last modified: 8/28/2015
Contributors: Qing Zhu
- Initial prototype of the N-COM model has been developed and tested in MATLAB.
- The N-COM model is being integrated in ACME
Planned Verification and Unit Testing
Verification and Unit Testing: Benchmarking
Date last modified: 8/28/2015
Contributors: Qing Zhu
ACME with N-COM codes will be evaluated using ILAMB benchmarking package.
Planned Validation Testing
Validation Testing: Model validate with global dataset
Date last modified: 8/28/2015
Contributors: Qing Zhu
ACME with N-COM codes, will be validated against global scale nitrogen/phosphorus fertilization experiments, across multiple ecosystems.
Planned Performance Testing
Performance Testing: short-description-of-testing-here
Date last modified:8/28/2015
Contributors: Qing Zhu