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Title:
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Integrating the Biogeochemical Transport and Reaction module into ALM
Requirements and Design
ACME Land group
Group
Date: 08/31/2015
Summary
soil biogeochemistry is an integrated system that includes biogeochemical reactions occurring in the presence of multiphase transport of chemical species and biological organisms. The traditional modeling approach that treats the soil biogeochemistry as a single soil layer has proven inadequate to resolve the important processes and empirical measurements. Therefore, to enable ALM to better resolve the soil biogeochemistry and link ALM predictions closer to empirical measurements, the Biogeochemical Transport and Reaction module is integrated.
Requirements
Requirement: name-of-requirement-here
The requirements for BeTR module include:
- An operator splitting based treatment of various transport and reaction processes.
- A reaction based formulation of generic soil biogeochemical processes.
- A consistent numerical treatment to ensure mechanistic consistencies.
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:
Contributors:
(add your name to this list if it does not appear)Jinyun Tang
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 generic mathematical formulation of BeTR is
d(Cs+Cw*theta+Cg*epsilon)/dt=diffusion+advection+R ...(1)
where
Cs = solid phase of a given tracer
Cw= aqueous phase of a given tracer
Cg=gaseous phase of a given tracer
R = biogeochemical reactions, gas addictions, biotic and abiotic subsurface/later transport.
The diffusion is solved using an implicit scheme, advection is used using the semi-lagrangian approach, and R is solved with ODE solvers.
Design and Implementation
Implementation: short-desciption-of-implementation-here
Date last modified:
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?
08/31/2015
Contributors:
(add your name to this list if it does not appear)Jinyun Tang
- ALM-BeTR will be written using OOP design and installed as a separate directory under the ALM repository.
- ALM-BeTR will include its own code library to handle various substrate competition processes and appropriately refer to standard numerical packages, such as BLAS, LAPACK.
Planned Verification and Unit Testing
Verification and Unit Testing: short-desciption-of-testing-here
Date last modified:
08/31/2015
Contributors:
(add your name to this list if it does not appear)Jinyun Tang
- Unit testing will
- be conducted to compare numerical simulations with analytical solutions
- Mock test will be conducted to ensure the logical order of the model is constantly and correctly done.
- On/off test will be conducted to make sure BeTR does not affect other soil biogeochemical formulations are currently used in ALM.
Planned Validation Testing
Validation Testing: short-desciption-of-testing-here
Date last modified:08/31/2015
Contributors: (add your name to this list if it does not appear)
- The reaction-based BeTR-BGC will be compared with the default Century-BGC in ALM.
- The output from BeTR-BGC will be benchmarked using ILAMB.
Planned Performance Testing
Performance Testing: short-desciption-of-testing-here
Date last modified:08/31/2015
Contributors:
(add your name to this list if it does not appear)Jinyun Tang
- The ACME timing logs will
- be implemented in the ALM-BeTR to obtain performance metrics and compared with that of the default ALM.