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The Design Document page provides a description of the algorithms, implementation and planned testing including unit, verification, validation and performance testing. Please read  Step 1.3 Performance Expectations that explains feature documentation requirements from the performance group point of view. 

Design Document

Overview table for the owner and an approver of this feature

1.Name
2.OwnerJinyun Tang
3.Created08/31/2015
4.Equ(tick) - c
5.Ver(tick) - c
6.Perf(warning)
7.Val(warning)
8.Approver
9.Approved Date
 Click here for Table of Contents ...

Table of Contents

 

 

 

Title: Integrating the Biogeochemical Transport and Reaction module into ALM

Requirements and Design

ACME Land group
 Group

Date: 08/31/2015
 

Summary

The 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. 
 BeTR is a highly modular code that deals with multiphase transport for an arbitrary number of chemical species. It explicitly considers transport through multiphase diffusion, aqueous advection, parenchyma transport, and gas advection. It provides template to build generic reaction-based soil biogeochemical formulations, and solves the multi-nutrient limitations consistently. It adopts the polymorphism design to allow ALM using multiple formulations of soil biogeochemical processes, which therefore provide hierarchical analysis on how structural difference would affect the soil biogeochemical model performances.

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: 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: 08/31/2015

Contributors: 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: 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: 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.

 

 


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