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Homogenization 2.0 #254

Merged
merged 13 commits into from
Nov 20, 2024
Merged

Homogenization 2.0 #254

merged 13 commits into from
Nov 20, 2024

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marcadella
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@marcadella marcadella commented Nov 14, 2024

See issue #253

  • fix negative N pools
  • improve numerical stability (preventing some segfaults from happening)
  • Fix reporting of some diagnostics that were missed.

- Update vignettes
- Save full model outputs for Biomee (including site level)
- Move BiomeE integration test
- Change QMD -> QMD12
- Remove unused parameters for BiomeE (outputhourly, outputdaily, dist_frequency, do_reset_veg)
@marcadella marcadella linked an issue Nov 14, 2024 that may be closed by this pull request
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@marcadella
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@fabern I haven't updated the documentation for P-model (point 4 in the old pull-request). I don't know p-model at all. I also completely re-written data_format.Rmd. To avoid back and forth, I propose that you just commit the changes you wish directly in this branch (253).

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fabern commented Nov 18, 2024

Thanks @marcadella, most of my suggested changes to the order of the docs were already done by you in commit (499b2c2), I now made small, last adjustments in (63f29b3).

This is ok to cover point 4.

marcadella added 6 commits November 18, 2024 14:22
…rection of psoil_sl leading to negative values.
- Fix post mortality metrics never set in annual_diagnostics
- Fix  annualfixedN never updated
Ag_l exploding causes Psyn, Gpp, plabl%c12, C_push, C_growth, dBSW, cc%DBH and oldcc%crownarea to be NaN

Note that if this removes the segfault, we have not treated the root cause of the issue causing Ag_l to explode in the first place.
@marcadella marcadella marked this pull request as ready for review November 20, 2024 09:44
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@stineb The models are now working fine using the N inorg refill hack (cf #256 ).

@marcadella marcadella requested a review from stineb November 20, 2024 09:46
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Looks good from a quick glance. Thanks!

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ok

@stineb stineb merged commit 840de54 into master Nov 20, 2024
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@stineb stineb deleted the 253-homogenization-20 branch November 20, 2024 16:42
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Homogenization 2.0
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