Atlantis release updates

Updating to more recent versions of the source code is not always straightforward. To get your model to run often requires including additional parameters (with default values) in several of the input parameter (.prm) files. Here we describe a list of changes required when updating to stable versions of the model. Each release assumes all prior release changes have been implemented.

v6698

biology.prm

Flags to activate temperature dependent movement and recruitment

> flagtempdepend_move 0
> flagtempdepend_reprod 0

run.prm

Flag is used to maintain old plankton mortality assumptions (from very early code versions that persisted as potential bug into newer models). Turning it on zeroes out phytoplankton mortality and only allows for lysis in phytoplankton.

> flag_replicated_old_PPmort 0

harvest.prm

Related to companion species. Catch of one species results in bycatch of another

> K_max_co_sp 0
> max_co_sp_XXX 0

migrations.csv

One additional column is required (17 columns total)

• ReprodAllowed is whether individuals participating in this migration can spawn when they reach maturity (1 = yes, 0 = no). If set to 0 then in multi year spawners (like salmon), the individuals will not spawn even if they reach adult ages during that migration.

v6681

biology.prm

Indicate which method to deal with temperature scalars. setting to zero uses a simple Q10 based correction using 15'C reference

> q10_method_XXX 0

v6678

biology.prm

Related to movement of individuals when conditions are outside their tolerance

> flagenviro_displace 0
> flagenviro_kill 0

Value variablity (sigma) for species recruitment around mean level and flag to turn it on

> XXX_norm_sigma 0
> XXX_flag_recruit_stochastic 0

migrations.csv

Three additional columns are required (16 columns total)

• PartialExit - whether for the multi-year migrations only some of the age group leaves and for those that don’t leave they remain resident rather than attempt to leave in subsequent years.
• MinAgeLeave - if the model has a mix of leaving and resident in multi-year migrations (i.e.PartialExit = 1) this is the youngest cohort leaving. If only the youngest age group migrating set this to 0.
• MaxAgeLeave if the model has a mix of leaving and resident in multi-year migrations (i.e.PartialExit = 1) this is the oldest cohort leaving. If only the youngest age group migrating set this to 0 (or other juvenile residents will leave in subsequent years).

harvest.prm

Harvest control rule setting for guilds rather than species

> do_sumB_HCR 0 

v6670

Atlantis now has the capability to interact with R. The Dockerfile has changed to reflect this. Additional lines are required in the PreRules.am file to point to the location of the R installation.

PreRules.am

Make sure these lines are not commented out and comment out any other lines with reference to the variables R_HOME and R_BASE

> R_HOME = /usr/lib/R
> R_BASE = /usr/lib/R 

harvest.prm

Flag to indicate whether to use Redus Harvest control rule (Specific to Holly Perryman)

> usingRedus_R_HCR 0
> useMultispAssess 0 (However omitting it does not make a difference for NEUS)

Assess.prm

> UsingRAssess 0 (However omitting it does not make a difference for NEUS)

If you are using the R functonality there are many more parameters that need to be included. If you are not, it is not necessary to include them

v6665

run.prm

Dumps total biomass (across every MIGID entry) from migration array into biomindx.txt. Previously while a migrator was outside the model, its biomass was not reported in the NetCDF output file

> flag_mig_in_bioindx 1 

biology.prm

The parameters flaglocalrecruitXXX and flagext_reprodXXX have been removed and added to the groups.csv file

groups.csv

Two additional columns are required

• ExternalReproduction - Indicates if the group spawn inside the model domain (0) or outside (1). Replaces flagext_reprodXXX parameter in biology.prm
• RecruitType - Indicates Recruitment. 0 = independent distribution (use recruit_hdistrib), 1 = at parental locations, 2 = external (into Migration Array), 3 = using a forced larval dispersal matrix, 4 = salmonid lifestyle where recruit into the model before then migrating out again as a juvenile (returning later as an adult) Replaces flaglocalrecruitXXX parameter in biology.prm

harvest.prm

Added XXX_mFC_endage to mirror XXX_mFC_startage. Confluence blog. NEUS forces catch so these are ignored.

v6645

run.prm

Relevant to Australia model. Maximum number of species in basket quota

> K_num_basket 1 

Flag indicating whether warning messages about spawn and movement being environmentally constrained are activated

> flagenviro_warn 0

harvest.prm

Required for each species (XXX) in the model followed by nn, the number of fleets in the model.

spawn_closure_XXX nn
Vector of zeros and ones of length nn

eg. for Mackerel (MAK) with 28 fleets in the model

spawn_closure_MAK 28
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 

initial conditions nc

The nc file will need to be edited using ncdump, ncgen functions from NetCDF libraries.

`DayLight` variable will need to be added

Copy all entries related to Light found in the nc file and name them DayLight. There will probably be a light entries for each forced lower trophic group.

biology.prm

Contaminants added. Not used in neus-model.

v6631

run.prm

Flag indicating polar - so there will be 24 hrs of daylight/night seasonally

flagIsPolar 0 

forcing.prm

Prior to v6631 each tracer had a single entry of the form: eg, for tracer Diatom_N

Diatom_N_use_resets 0

This line is now replaced by multiple lines. One line for each forcing file. For example if the model is forced with 10 years of Diatom_N data, the entries would have the form:

Diatom_N_File0.use_resets 0 
Diatom_N_File1.use_resets 0
Diatom_N_File2.use_resets 0
Diatom_N_File3.use_resets 0
Diatom_N_File4.use_resets 0
Diatom_N_File5.use_resets 0
Diatom_N_File6.use_resets 0
Diatom_N_File7.use_resets 0
Diatom_N_File8.use_resets 0
Diatom_N_File9.use_resets 0
Diatom_N_File10.use_resets 0

v6626

run.prm

flag_migration_on 0
flag_contam_sanity_check 0

forcing.prm

Diatom_N_use_resets 0
PicoPhytopl_N_use_resets 0 
Diatom_S_use_resets 0
DinoFlag_N_use_resets 0 
Lab_Det_N_use_resets 0 

Forcing movement parameters (see v6598 for details). Not used in NEUS model

biology.prm

By default mat_transition_thresh should be something high like 0.99 and juv_transition_thresh something lower like 0.1 or 0.5 etc, so this only comes into play when the majority of the adult population is outside the model and juveniles not (v6617)

juv_transition_thresh 0.1 
mat_transition_thresh 0.99 

lines containing XXX need to be replicated for each species in the model

flagkeep_plusgroupXXX 0

Migration.csv

Migration file required specifying which species migrate and when. See the blog for details n how to structure this file

groups.csv

Two additional columns are required.

• NumMigrations - Indicating the number of migrations initiated per calendar year.
• MultiYrMigrations - A value of 1 indicates at least one of the migrations started per year can last for many years

RunAtlantis.sh

Need to add the migrations.csv to the Run command

... -m migrations.csv ...

v6599

Changes required in configure.ac before success in building

• AC_PREREQ([2.71]) to AC_PREREQ([2.64])
• Comment out line: AC_CHECK_INCLUDES_DEFAULT

forcing.prm

use_pollutantfiles 0

run.prm

flag_pollutant_factors 0
flag_pollutant_impacts 0

harvest.prm

flagKeepZeroCatchTS 0

v5680

biology.prm

lines containing XXX need to be replicated for each species in the model

rugosity_bozec_a 16.0
rugosity_bozec_b 1.5
rugosity_bozec_c 8.0
rugosity_bozec_d 3.0
XXX_cohort_recruit_entry 0

harvest.prm

discardTAC 0 

v6536

This is the version used for the initial release of the Northeast United States Atlantis model