Atlantis_TODO - Bec’s task list

See below for more information on tasks.

Bec to do list

100% of the tasks completed

	Flexible fisheries	Medium
	Move the assessment data structures into the atAssessModule	Medium
	Move the management data structures into the atManageModule	Medium
	Move the physics data structures into the atPhysicsModule	Medium
	Simpilfy the diet availability code. At present there are two arrays bm->pSPageeat and FunctGroupArray[sp_id].pSPEat. It would be good to make these into a single array that is calculated at the start of the run. This would simplify the getPreyAvail function.	Medium

Small Tasks

Comment the new input code and explain how it all works and how to add new parameters.
Change all atlantis comments to doxygen format
Get all error messages to stdout or stderr

Change the migration code to not loop over 1 ->3 for the migration groups but to loop over 1 - K_max_num_mig.

get trelib linking as a static lib not a dll.

This is done. Had to create a seperate static library visual studio project to build from there. Now all that is required is the tre.lib and the tre-config.h and regex.h files.
In doing this I have also built the atlantis visual studio project in such a way that it can be given to another developer - they can then just open it and the code will build. The original complex set of instructions needed to build atlantis are no longer needed.

Data restructure - move the species params into the function group array. Move the funct group array into the bm.

To resolve post species param restructure: - Will need to check that all of the parameters are read in for the different cohorts in
ecol_readCohortSpeciesParam(). - Need to look into the limits on number of time a group can migrate in/out of the model domain. Want these restriction to be removed. - Need to get rid of spNAME and use the code read in. - Need to merge the Spawn_Now and Inv_Spawn_Now arrays. - Any models that are using jPWN or jCEP are seperate groups will now need to be rewritten. - The jmL_id and mL_id species parameters really need to be sorted. A nicer was of doing this would be to have a single parameter and store a value for each cohort. For the verts i could
check the maturity age when the model is started and set the juv cohorts to the juv value and the adults cohorts to the adult value. - fisheater_id and catcheater_id could potentially be a cohort dependant species parameter. It is based on the values in the pSPEat array. Need to check into this later. I think they are but these values are only used for the vert groups so i’ll ignore this issue. Perhaps in the future we might want to look into changing this. - That bm->DebugInfo does not need to have cohort level data. Should it be a sum of the cohort data? At present it is not in the inverts but it is for the verts.