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Atlantis ecosystem model

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Welcome to the Atlantis marine ecosystem model discussion group. Here you can ask and answer questions related to the use of the model, share your ideas, projects and new publications, and discuss the science behind the model. This discussion group does not replace the Atlantis Wiki, but (hopefully) complements it

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cha...@oregonstate.edu, Fulton, Beth (Environment, Hobart)2

9/15/25

Questions about fixes/edits to sediment-related processes and biogeochemistry

OFFICIAL G'day Very happy for you to play with that bgc. It is reflective of how sediment

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Questions about fixes/edits to sediment-related processes and biogeochemistry

OFFICIAL G'day Very happy for you to play with that bgc. It is reflective of how sediment

9/15/25

Hem Nalini Morzaria Luna - NOAA Affiliate, Fulton, Beth (Environment, Hobart)2

4/27/25

Light application in Atlantis?

G'day In a way all models do because if you'd have enough light the phytoplankton and

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Light application in Atlantis?

G'day In a way all models do because if you'd have enough light the phytoplankton and

4/27/25

Andrew Beet - NOAA Affiliate, Fulton, Beth (Environment, Hobart)2

4/23/25

vertNIGHT and vertDAY redistribution

G'day The assumption is that it is always day. In case anyone is interested, with ttimesteps per

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vertNIGHT and vertDAY redistribution

G'day The assumption is that it is always day. In case anyone is interested, with ttimesteps per

4/23/25

siem...@gmail.com

3/21/25

Changes in species fishing mortality when using dynamic effort

Hi everyone, I want to run some simple scenarios where fishing pressure of 1 species increases with

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Changes in species fishing mortality when using dynamic effort

Hi everyone, I want to run some simple scenarios where fishing pressure of 1 species increases with

3/21/25

Fulton, Beth (Environment, Hobart)

2/27/25

G'day For those who have updated form the Trunk since December please do a fresh update I had

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G'day For those who have updated form the Trunk since December please do a fresh update I had

2/27/25

Kévin Cazelles

2/24/25

Guidance on Clearance Rate, MUM, Prey Availability, KUP, KLP, and Mortality Rates

Dear Atlantis Community, We are encountering similar challenges to those discussed in these threads:

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Guidance on Clearance Rate, MUM, Prey Availability, KUP, KLP, and Mortality Rates

Dear Atlantis Community, We are encountering similar challenges to those discussed in these threads:

2/24/25

jaco...@gmail.com, Fulton, Beth (Environment, Hobart)3

2/18/25

another segmentation fault

here are the links to those files, Beth. If anyone else would like access I can grant it. This should

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another segmentation fault

here are the links to those files, Beth. If anyone else would like access I can grant it. This should

2/18/25

jaco...@gmail.com

2/14/25

I just started saving the information that is printed to the screen while running Atlantis and am

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I just started saving the information that is printed to the screen while running Atlantis and am

2/14/25

Hem Nalini Morzaria Luna - NOAA Affiliate, Fulton, Beth (Environment, Hobart)6

1/29/25

Problem with SP_Concern at_harvest parameter

G'day Can you please share your csv file so I get a better understanding of the mix of isFished

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Problem with SP_Concern at_harvest parameter

G'day Can you please share your csv file so I get a better understanding of the mix of isFished

1/29/25

Tom Ihde, Fulton, Beth (Environment, Hobart)3

1/24/25

still stuck on first timestep

Problem resolved. Beth figured out what we were doing wrong. CAM2 is now running again, after only 8

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still stuck on first timestep

Problem resolved. Beth figured out what we were doing wrong. CAM2 is now running again, after only 8

1/24/25

1/21/25

seeking colleague for California Current atlantis/stock assessment project

Hello Atlantis community -- please share this job advertisement to colleagues who might be interested

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seeking colleague for California Current atlantis/stock assessment project

Hello Atlantis community -- please share this job advertisement to colleagues who might be interested

1/21/25

Kévin Cazelles, Isaac Kaplan - NOAA Federal2

1/15/25

Memory Allocation Issue in Atlantis Model Version 6698

Hi Kevin, In v6718, I can confirm that I have the same as the first line you noted: bm->BiTAC_sp =

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Memory Allocation Issue in Atlantis Model Version 6698

Hi Kevin, In v6718, I can confirm that I have the same as the first line you noted: bm->BiTAC_sp =

1/15/25

Tom Ihde, … Cecilie Hansen4

1/14/25

hung up at the start of the model run

Hi tom, i've seen this before (snow crab eating infinite amounts of polar bear) - i'm trying

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hung up at the start of the model run

Hi tom, i've seen this before (snow crab eating infinite amounts of polar bear) - i'm trying

1/14/25

ilaria.s...@utas.edu.au, Joseph Caracappa - NOAA Federal2

1/13/25

Forcing files clarification

Generally the forcing files need to match the units of the output variable so it depends. Some

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Forcing files clarification

Generally the forcing files need to match the units of the output variable so it depends. Some

1/13/25

Fulton, Beth (Environment, Hobart), … jaco...@gmail.com5

12/13/24

Wiki and SVN update

Hi Beth To answer your questions... I think I just need trunk access, I have the older versions I use

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Wiki and SVN update

Hi Beth To answer your questions... I think I just need trunk access, I have the older versions I use

12/13/24

Robert Gamble - NOAA Federal, … matteo.sinerchia16

11/27/24

Weird recruitiment issue

Hi Beth, thanks a lot. I have sent you the credentials to access my unix machine. Cheers, Matteo. Il

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Weird recruitiment issue

Hi Beth, thanks a lot. I have sent you the credentials to access my unix machine. Cheers, Matteo. Il

11/27/24

Fulton, Beth (Environment, Hobart)

11/25/24

G'day It seems CSIRO has (frustratingly) discontinued external access to CSIRO wiki system. I am

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G'day It seems CSIRO has (frustratingly) discontinued external access to CSIRO wiki system. I am

11/25/24

Cecilie Hansen, Fulton, Beth (Environment, Hobart)3

11/21/24

Extreme levels of nutrients in a few polygons

Hi beth! they are similar, or lower. input/output variation seem reasonable, and are to layers that

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Extreme levels of nutrients in a few polygons

Hi beth! they are similar, or lower. input/output variation seem reasonable, and are to layers that

11/21/24

ilaria.s...@utas.edu.au

11/7/24

A 3d map of Atlantis domains!

Hello Atlantis community, This is quite a different problem from the usual - I have been toying

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A 3d map of Atlantis domains!

Hello Atlantis community, This is quite a different problem from the usual - I have been toying

11/7/24

Vidette McGregor, Robert Wildermuth3

9/12/24

Carbon sequestration and trackAtomicRatio

Hi Robert Thanks for the prompt response! I'm in the fairly early stages of thinking about this,

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Carbon sequestration and trackAtomicRatio

Hi Robert Thanks for the prompt response! I'm in the fairly early stages of thinking about this,

9/12/24

Hem Nalini Morzaria Luna - NOAA Affiliate, Fulton, Beth (Environment, Hobart)3

8/20/24

Segmentation fault

Beth: I am attaching the output of the verbose 5 option, I still can't tell where the problem is.

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Segmentation fault

Beth: I am attaching the output of the verbose 5 option, I still can't tell where the problem is.

8/20/24

Cecilie Hansen, Fulton, Beth (Environment, Hobart)3

8/9/24

Excessive nutrient levels?

G'day Glad to hear you sorted it. If future if anyone hits this issue and its not an in.nc oops

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Excessive nutrient levels?

G'day Glad to hear you sorted it. If future if anyone hits this issue and its not an in.nc oops

8/9/24

ilaria.s...@utas.edu.au, … Porobic Garate, Javier (Environment, Hobart)8

7/23/24

forcing file issue

Hi Ilaria, To clarify further, using the same values for the fillValue and missing_value properties

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forcing file issue

Hi Ilaria, To clarify further, using the same values for the fillValue and missing_value properties

7/23/24

Joseph Caracappa - NOAA Federal, … Isaac Kaplan - NOAA Federal7

7/19/24

Spatial Biomass and Density Dependence

These are neat topics -- both the idea of turning on the foraging movement, and the comparison of

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Spatial Biomass and Density Dependence

These are neat topics -- both the idea of turning on the foraging movement, and the comparison of

7/19/24

6/27/24

respiration example parameters?

Hi Atlantis gang, Have you implemented respiration for Atlantis? If so, would you be willing to share

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respiration example parameters?

Hi Atlantis gang, Have you implemented respiration for Atlantis? If so, would you be willing to share

6/27/24

Fulton, Beth (Environment, Hobart)

6/24/24

G'day For anyone who has updated to the latest revision (basically since start of April) please

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G'day For anyone who has updated to the latest revision (basically since start of April) please

6/24/24

ilaria.s...@utas.edu.au, Fulton, Beth (Environment, Hobart)3

6/8/24

Larvae and YOY troubles

Hello Beth, Thanks for your reply! I turned on flag_sanity_check, and still got some groups with

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Larvae and YOY troubles

Hello Beth, Thanks for your reply! I turned on flag_sanity_check, and still got some groups with

6/8/24

Hem Nalini Morzaria Luna - NOAA Affiliate, … Fulton, Beth (Environment, Hobart)3

6/3/24

Large changes in model behavior after version 6708

G'day What do you think has changed in demography that is causing the change in numbers/biomass?

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Large changes in model behavior after version 6708

G'day What do you think has changed in demography that is causing the change in numbers/biomass?

6/3/24

5/24/24

R tools added to public repo - making pred-prey overlap map

Hei! I have uploaded a R script file that I developed for making a map that shows the spatial

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R tools added to public repo - making pred-prey overlap map

Hei! I have uploaded a R script file that I developed for making a map that shows the spatial

5/24/24

jaco...@gmail.com, … Hem Nalini Morzaria Luna - NOAA Affiliate4

5/10/24

something amiss with migration in 6702?

Hi, following up if you have found the issue? We see anomalous behavior in the first 5 years of our

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something amiss with migration in 6702?

Hi, following up if you have found the issue? We see anomalous behavior in the first 5 years of our

5/10/24

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