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v2.2.0 Age Structure and v6681 Code Update #244

Merged
merged 178 commits into from
Mar 18, 2024
Merged

v2.2.0 Age Structure and v6681 Code Update #244

merged 178 commits into from
Mar 18, 2024

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jcaracappa1
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@jcaracappa1 jcaracappa1 commented Mar 13, 2024 •
edited by andybeet
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Uses Atlantis codebase v6681

Summary

  • Contains all pull requests from #228 to #243
  • Updated age structure of functional groups with associated age-based parameter changes in neus_groups.csv, at_biology.prm, at_harvest.prm, and neus_init.nc
  • Updated code-base to v6681, with additional new parameters and a new neus_migrations.csv
  • General calibration of v6681 biology.prm to match previous release calibration criteria
  • Bug fixes and development of cloud calibration workflow

andybeet and others added 30 commits September 30, 2023 12:13
@andybeet
rearranged at_harvest.prm for easier readability and calibration.
f5448f2 
- Follows order of manual
@andybeet
reorg effort displacement params
2a8af4f
@andybeet
Vertical, positional and habitat scalars of the fishing effort
9e7280a
@andybeet
Fisheries gear selectivity, swept area and conflict
22ec0b3
@RGamble1
Initial v6665 run
08327f3
@RGamble1
Initial run
67c268f
@andybeet
add fishieries discarding params
09054cd
@andybeet
added temporal changes in harvest
54e6b4b
@andybeet
add management, TAC params
b05d538
@jcaracappa1
sample setup file for cloud calibration workflow
747ed33
@jcaracappa1
sample setup file for cloud calibration workflow
17dee81
@jcaracappa1
Merge branch 'cloud_calibration' of https://github.com/NOAA-EDAB/neus…
6959c84 
…-atlantis into cloud_calibration

# Conflicts:
#	diagnostics/cloud_calibration_setup_example.csv
@jcaracappa1
Merge branch 'cloud_calibration' of https://github.com/NOAA-EDAB/neus…
076a4c2 
…-atlantis into cloud_calibration

# Conflicts:
#	diagnostics/cloud_calibration_setup_example.csv
@jcaracappa1
Merge branch 'cloud_calibration' of https://github.com/NOAA-EDAB/neus…
e6d2f4f 
…-atlantis into cloud_calibration

# Conflicts:
#	diagnostics/cloud_calibration_setup_example.csv
@jcaracappa1
Mortality cases complete
77afbb3
@andybeet
Add economics section
7fc4698
@jcaracappa1
finished script & tested
6d1877f
Merge branch 'cloud_calibration' of https://github.com/NOAA-EDAB/neus…
cc85366 
…-atlantis into cloud_calibration
Plotting Script and Calibration Script bug fixes
95091a9
@andybeet
add contents to harvest.prm
6aeaf4d
@RGamble1
Fixed migratory groups
35c195b
@RGamble1
Change output flag and periodicity
c3e9114
@jcaracappa1
Changed age-based parameters to reflect fishbase and NOAA data
20c0a96 
- AgeClassSize
- NumAgeClasses
- age_mat
- li_a
- li_b
@jcaracappa1
add assimilation efficiency
df26885
@jcaracappa1
biomass comparison plots for cloud calibration workflow
7befdc7
@jcaracappa1
temporarily removed new length-weight (will test separately)
3fcb78f
@jcaracappa1
fix hanging tab
69f833b
@jcaracappa1
code to rescale mum/C for new age classes
6403ecc
@jcaracappa1
tools for generating new age structure
3161010
@jcaracappa1
add stop condition for incompatible Type entry
ddd35a6
jcaracappa1 and others added 11 commits March 6, 2024 16:48
@jcaracappa1
Merge branch 'jcc_6681_calibration' of https://github.com/NOAA-EDAB/n…
6f72455 
…eus-atlantis into jcc_6681_calibration
@jcaracappa1
merge fix
d0e4381 
Merge branch 'jcc_6681_calibration' of https://github.com/NEFSC/READ-EDAB-neusAtlantis into jcc_6681_calibration

# Conflicts:
#	Setup_Files/cloud_v6681_calib_6.csv
@jcaracappa1
merge
c8d31c4 
Merge branch 'jcc_6681_calibration' of https://github.com/NEFSC/READ-EDAB-neusAtlantis into jcc_6681_calibration

# Conflicts:
#	Setup_Files/cloud_v6681_calib_6.csv
@jcaracappa1
Merge branch 'jcc_6681_calibration' of https://github.com/NOAA-EDAB/n…
457b273 
…eus-atlantis into jcc_6681_calibration
@jcaracappa1
biomass-at-age plot for run scripts
4a58403
@RGamble1
Merge pull request #241 from NEFSC/jcc_6681_calibration
0656e33 
Jcc 6681 calibration
@jcaracappa1
cloud_calib_6b
99a0f99
@jcaracappa1
cloud_calib_v6681_6b
e6e2b6f
@RGamble1
Merge pull request #242 from NEFSC/jcc_6681_calibration
0a09bce 
Jcc 6681 calibration
@RGamble1
Update at_run.prm (Set scalar to 10x for cod's initial biomass)
1ae7f6e
@andybeet
Merge pull request #243 from NEFSC/RJG_6681_Calibration_1_29_24
0c57f11 
Rjg 6681 calibration 1 29 24
@jcaracappa1
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I added a brief summary. We should expand as needed. This is where we get the release notes from

@andybeet
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I'm running dev, will then run full post processing , and copy to google drive

@jcaracappa1
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Found and fixed error in at_biology.prm BHbeta_WHK was 3.25+14 instead of 3.25E14
Can anyone figure out what the diffs are for the at_harvest.prm. It says they're in the thousands of lines.

@andybeet
Revert "Merge branch 'andy_communities' into dev_branch"
2950888 
This reverts commit 00fbb75, reversing
changes made to 0c57f11.

Revert harvest file format changes
@jcaracappa1
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After fixing the typo if BHalphaWHK from "3.25+14" to "3.25E14" it caused WHK to crash. I'm proposing we keep the "incorrect" version since it does result in normal recruitment and diagnose in next release.
image

@andybeet
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andybeet commented Mar 18, 2024 •
edited
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i agree. If i look at the diff, it looks like it was changed from E+14 to E14 which seems the opposite of what you'd want. unless i am reading that wrong. Was the change made in error?

@jcaracappa1
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There was no "E" previously.

@RGamble1
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This looks good to me - except the weird WHK recruitment parameter. But I agree with Joe, we can fix in the next release

RGamble1
RGamble1 approved these changes Mar 18, 2024
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This looks good to me except for the strange recruitment parameter for WHK. But I agree to fix it in the next release.

@andybeet andybeet self-requested a review March 18, 2024 17:08
andybeet
andybeet approved these changes Mar 18, 2024
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looks good

@andybeet andybeet merged commit 1c94a94 into master Mar 18, 2024
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@jcaracappa1 @andybeet @RGamble1