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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

 Click here for instructions to fill up the table below ......

The first table in Design Document gives overview of this document, from this info the Design Documents Overview page is automatically created.

In the table below, 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation

  • Equations: Document the equations that are being solved and describe algorithms
  • Verification Plans: Define tests that will be run to show that implementation is correct and robust. Involve unit tests to cover range of inputs as well as benchmarks.
  • Performance expectations: Explain the expected performance impact from this development
  • Validation Plans: Document what process-based, stand-alone component, and coupled model runs will be performed, and with what metrics will be used to assess validity

Use the symbols below (copy and paste) to indicate if the section is in progress or done or not started.

In the table below, 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation,   (tick) - completed, (warning) - in progress, (error) - not done

 

Overview table for the owner and an approver of this feature

1.Description

Interactions with the surface models (Sea Spray organic matter)
2.OwnerSusannah Burrows
3.Created
4.Equ(tick)
5.Ver(error)
6.Perf(error)
7.Val(error)
8.Approver
9.Approved Date
V1.0Pending
 Click here for Table of Contents ...

Table of Contents

Title: Interactions with the surface models (Sea Spray, DMS)

Requirements and Design

ACME Atmosphere Group

Date: 09-16-2015

Summary

The purpose of this section is to summarize what capability is to be added to the ACME Ocean and Ice system 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.”

 

The new v1 capability will read in netCDF files containing ocean surface distributions of marine macromolecules (lipids, polysaccharides, and proteins) and produce

Requirements

Requirement 1: Calculation of marine organic emissions from offline fields produced from marine biogeochemistry models

Date last modified:  
Contributors: Susannah Burrows, Scott Elliott (Unlicensed), Richard Easter (Unlicensed)


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 1a: Formulation of relationship between ocean surface organic concentrations and organic mass fraction of emitted sea spray aerosol

Date last modified:Dec 2014
Contributors: Susannah Burrows, Scott Elliott (Unlicensed), Phil Rasch (pnl.gov)

See Burrows et al., 2014, ACP.

Burrows, S. M., Ogunro, O., Frossard, A. A., Russell, L. M., Rasch, P. J., and Elliott, S. M.: A physically based framework for modeling the organic fractionation of sea spray aerosol from bubble film Langmuir equilibria, Atmos. Chem. Phys., 14, 13601-13629, doi:10.5194/acp-14-13601-2014, 2014.

Design solution 1b: Formulation of assumed relationships between marine organic mass fraction and particle size and mixing state

Date last modified: Aug 2015
Contributors: Susannah Burrows

Some initial testing is documented here: /wiki/spaces/ATM/pages/32374899.

For an initial implementation, organic mass fraction calculated according to Burrows et al (2014) will be assumed to apply directly to Aitken mode and accumulation mode aerosol.  Emissions within MAM4 will be implemented as a default configuration, with all marine organics combined into a single species, adding 3 advected tracers to the MAM4 scheme.  A switch/parameter will be implemented to control mixing state (internal/external) of accumulation mode emissions.

Design and Implementation

Implementation 1a: Implementation of Burrows et al. 2014 marine organic aerosol emissions with MAM9 aerosols

Date last modified: 09/15/2015
Contributors: Susannah Burrows, Richard Easter (Unlicensed), Xiaohong Liu (add your name to this list if it does not appear)

New emissions formulation will be implemented within seasalt_model.F90.  Organic mass fraction of emitted aerosol will be calculated using static netCDF files describing the distribution of organic molecules in surface ocean water, provided as netCDF files.  The distributions will be obtained from low-resolution ACME ocean BGC simulations if available; otherwise, older distributions from POP simulations will be used.  Emitted aerosol mass and number will be added to modes 1 (accumulation), 2 (Aitken) and 4 (primary organic), and emitted sea salt mass will be reduced if appropriate (depending on mixing state).

Implementation 1b: Implementation of alternate marine organic aerosol emissions parameterizations

Date last modified: 09/15/2015
Contributors: Susannah Burrows (add your name to this list if it does not appear)

Implement parameterizations by Rinaldi, Gantt, and constant emissions (based on Quinn et al. 2014) for benchmarking / comparison purposes.
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?

 


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