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
In the table below 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation, 
- competed, 
- in progress, 
- not done
Overview table for the owner and an approver of this feature
1.Description | Corrects inadequacies in sea ice nitrogen dynamics |
| 2.Owner | Nicole Jeffery |
| 3.Created | 08/26/2019 |
| 4.Equ | |
| 5.Ver | |
| 6.Perf | |
| 7.Val | |
| 8.Approver | |
| 9.Approved Date |
Title: Improved nitrogen cycling in sea ice
Requirements and Design
E3SM Sea Ice Group
Date:Aug 26, 2019
Summary
The E3SMv1.1 CBGC simulations of sea ice biogeochemistry (BGC) drastically underestimate ice algal primary production in the Arctic. This is in large part due to biases in the upper ocean nitrate pool. However, sea ice algal primary production is also underestimated in the Southern Ocean, albeit not as drastically, where surface nutrients do not play a role. This suggests insufficiencies in our modelled biochemical interactions. Several studies (Fripiat et al. 2013, New insights into sea ice nitrogen biogeochemical dynamics from the nitrogen isotopes papers; Baer et al. 2015, Nitrogen uptake dynamics in landfast sea ice of the Chukchi Sea) point to dissolved organic nitrogen (DON) remineralization and nitrate production from nitrification as important nutrient sources for algal production. These sources are important for two reasons. First, DON is found in high concentrations in the polar oceans and, unlike nitrate, DON adsorbs to the ice crystals during sea ice growth and so can accumulate to high concentrations in the sea ice. Remineralization of DON produces ammonium which is readily taken up by ice algae, in fact, preferentially to nitrate. Thus DON remineralization provides a new and abundant source of nitrogen for ice algae that will almost surely mitigate our production biases. Second, nitrate produced from nitrification is distinct from the ocean source of nitrate because it is trapped in a biofilm which adsorbs to ice crystals (Deman et al. 2019, High production going along with respiration, Impact of bio-film formation for sea ice biogeochemistry, IGS Sea Ice Symposium). This process allows for build-up of nitrate in the sea ice brine, a feature observed in sea ice cores (Baer et al., 2015; Duarte et al., 2017 Sea ice thermohaline dynamics and biogeochemistry in the Arctic Ocean: Empirical and model results) but that is virtually impossible in our current model design.
The current model has a DON pool that follows the transport physics of adsorbing BGC tracers. Fluxes between ocean and sea ice have already been implemented. In terms of biochemistry, DON is produced in situ during algal mortality but there is no loss term to ammonium from remineralization. This term will be added and tuned based on observations. Nitrification is already implemented in the v1 model but with a default rate constant of zero. Observations indicate a rate constant of 0.046 per day. The impacts of the bio-film, however, still need to be added. This requires some minor coding to allow for adsorption of nitrate during the biogeochemical reaction process but not, as occurs for DON, during brine transport.
The purpose of this section is to summarize what capability is to be added to the E3SM through this design process. It should be clear what new code will do that the current code does not. Summarizing the primary challenges with respect to software design and implementation is also appropriate for this section. Finally, this statement should contain general statement with regard to what is “success.”
Requirements
Requirement: name-of-requirement-here
Date last modified: // date
Contributors: @ name (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 implementation and testing. Requirements should not discuss technical software issues, but rather focus on model capability. To the extent possible, requirements 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:// date
Contributors: (add your name to this list if it does not appear)
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.
Design and Implementation
Implementation: short-desciption-of-implementation-here
Date last modified: // date
Contributors: (add your name to this list if it does not appear)
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?
Planned Verification and Unit Testing
Verification and Unit 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?
Planned Validation Testing
Validation 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? 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?
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?