The Design Document page provides a description of the algorithms, implementation and planned testing including unit, verification, validation and performance testing.
Design Document
Title: Nutrient COMpetition (N-COM): a mechanistic treatment of plant-soil nutrient interactions
Requirements and Design
ACME Land Group
Date: 8/28/2015
Summary
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
The ACME Land Model N-COM code will be tested with historical 1850 simulations timing, and compared to baseline ALMv0 performance timing.