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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: short-description-of-proposed-solution-here
Date last modified:
108/
2028/2015
Contributors:
Gautam BishtQing 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.
- The governing PDE for flow in porous media is given as:
d/dt (rho * phi * sat) = - Div (rho * q) + Q ... (1)
where
rho = density of water, which is a function of pressure and temperature,
phi = porosity,
sat = liquid saturation
q = darcy flux
Q = source/sink of water- 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.
Div = divergence operator
- The Darcy flux is given by q = - k kr / mu * Del (P) ... (2)
where
k = permeability,
kr = relative permeability.
mu = viscosity,
P = liquid pressure
- Following discretization schemes are used to solve Eq(2):
- Spatial discretization: Finite volume, Temporal discretization: Backward Euler scheme , biomass density) through ECA formulation
- 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.
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
Design and Implementation
Implementation: short-desciption-of-implementation-here
Date last modified: 10/20/2015
Contributors: Gautam Bisht
- 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
Planned Verification and Unit Testing
Verification and Unit Testing: short-desciption-of-testing-here
Date last modified: 10/20/2015
Contributors: Gautam Bisht
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: 10/20/2015
Contributors: Gautam Bisht
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 will be tested against previously benchmark problems published.
- Additionally, VSFM will be tested against PFLOTRAN for certain benchmark problems.
Planned Performance Testing
Performance 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?
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