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Groundwork luluc (Biomee)#277

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marcadella wants to merge 107 commits intomastergeco-bern/rsofun:masterfrom preparation_lulucgeco-bern/rsofun:preparation_lulucCopy head branch name to clipboard

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Commits on Dec 12, 2024

• Implement dummy LULUC data structures

  

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Commits on Dec 13, 2024

• - Reworked internal data structures as groundwork for LULUC.

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• Merge branch 'master' into preparation_luluc

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• Fix doc

  

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• Fix doc

  

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• Wraper cleanup

  

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Commits on Dec 16, 2024

• Simplify interface (init_soil)

  

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• Simplify interface (params_tile)

  

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• Simplify interface (params_species)

  

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• Add name to init_lu

  

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• Fix doc

  

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Commits on Dec 17, 2024

• Remove unused code

  

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• Simplify interface

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• Fix doc

  

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• Minor

  

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• Implement LULUC outputs

  

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Commits on Dec 18, 2024

• Fix issue with parallel run (due to flattening of arrays of dim 1) and regenerate biomee outputs.

  

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Commits on Dec 19, 2024

• Fix doc and make deprecated falgs less verbose.

  

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• Fix issue with runread_biomee not being able to deal with missing columns.

  

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• Fix unit test hanging because spinup was engaged.

  

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• Split sofun_r in two separate modules

  

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• Major refactoring:

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• Fix test being verbose.

  

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• Fix broken biomee p-model test

  

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• Protect state from alteration in biosphere_annual

  

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Commits on Jan 6, 2025

• Remove unused code in get_steering

  

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• Code refactoring:

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• Implement outer loop for LULUC (so far, no effect on the pools)

  

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• fixup! Implement outer loop for LULUC (so far, no effect on the pools)

  

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• Add year in land use output, and fill in spinup too.

  

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• Add site info to myinterface to quiet down compile warning

  

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Commits on Jan 7, 2025

• Add one vegn tile per LU, keeping memory separated for each.

  

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• Minor: cleanup units and initializations

  

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• Minor: some more cleanup

  

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• Refactoring: use myinterface to get parameters rather than copying them in vegn.

  

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Commits on Jan 8, 2025

• Refactoring: minor clean-up (removed unused function reset_vegn_initial)

  

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• Refactoring: minor clean-up

  

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• Refactoring: minor clean-up

  

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• Factorize diagnostics out of cohorts

  

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• Removed flag update_annualLAImax as implementation was mutating parameters (bad practice) and not actually doing much anyways (simply capping underLAImax and LAImax after year 1).

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Commits on Jan 9, 2025

• Update news

  

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• Refactoring: use function do generate derived variables rather using variables in type.

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• Refactoring: factorize fast_fluxes in cohort

  

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• Refactoring: move cohort type to its own file. Functionalize in preparation for OOP

  

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Commits on Jan 10, 2025

• Refactoring: removed static variables in gpp

  

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• Refactoring: Move zeroing cohort function to cohort file

  

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• Refactoring: Use OOP in cohorts

  

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Commits on Jan 14, 2025

• Refactoring: Use linked lists

  

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Commits on Jan 15, 2025

• Refactoring: renamed remove -> remove_cohort

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• Add capacity to sort cohorts by both increasing or decreasing height.

  

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• Fix bug in annual_diagnostic

  

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• Fix initilizations: it is important to not initialise local variables in procedures within the declaration as it is performed only once!!

  

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• Fix bug during reproduction assigning wrong value to plabl

  

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Commits on Jan 16, 2025

• Make implementation cohort independent. Does not change the output but simplifies a lot the code.

  

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• Actually the previous commit changes slightly the outputs for p-model. The changes make much more sense the way it is done now : - damped the signal then distribute it to each layer, rather than th…

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• Make implementation cohort independent. Does not change the output but simplifies a lot the code.

  

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• Actually the previous commit changes slightly the outputs for p-model. The changes make much more sense the way it is done now : - damped the signal then distribute it to each layer, rather than th…

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• Minor

  

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• Quick fix cohorts order

  

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Commits on Jan 17, 2025

• Fix vegn_reproduction (wrong seed cumul computation)

  

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• Make cohort_can_be_merge symmetric

  

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• Add possibility to add to the tail

  

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• Rename next -> heap

  

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• Simplify implementation of relayer (avoid copying cohorts when not necessary)

  

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Commits on Jan 20, 2025

• Fix issue when number of cohorts goes beyon the allowed number. Graceful degradation by simply not outputting the extra cohorts in out_annual_cohorts

  

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• Fix issue with inserting cohorts in tail

  

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• Fix issue with relayer not sorting by height (was happening after setting the vegn heap to NULL()...)

  

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• Update the outputs (minor changes)

  

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• Merge branch 'preparation_luluc_linked_list' into preparation_luluc

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• Remove the fortran tests from project as it breaks CRAN checks (not allowed to use STOP or PRINT).

  

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Commits on Jan 21, 2025

• Just moving test calibaration biomee out of the way to check where the segmentation fault is

  

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• Removing gs leuning to check if p-model works

  

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  948159e

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• Fix segfault

  

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  a51b9fc

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• Fix segfault

  

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  c1fd08b

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• Minor

  

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  6ded769

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• Factorize allometric variables as functions

  

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• Replace obsolete ccID with the cohort's uid

  

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Commits on Jan 22, 2025

• Reset uid at start of simulation

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• Generic implementation of sort_cohort

  

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• Implement relayer in place and remove option to insert at the tail (would be too easy to end up with an infinite loop)

  

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Commits on Jan 23, 2025

• Implement killed_heap

  

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Commits on Jan 24, 2025

• Split abstract linked list

  

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• Use pointer comparison rather than uid

  

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• Make uid private

  

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• Add cohort_pool type as a linked list wrapper

  

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• Minor: rename some methods

  

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  51d21d0

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• make cohort stacks private

  

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• fix issue with duplicated uids (in cohort_list and killed_cohort_list)

  

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• Minor

  

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• Implement deadtree diagnostics

  

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Commits on Jan 27, 2025

• Refactoring: clearer separation between vegetation tile and vegetation processes.

  

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• Re-generate outputs. No major difference. See comment in test-model-runs.

  

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• Minor: remove un-necessary zeroing in gpp

  

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• Fix issue with deadtree pools being mis-labeled

  

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Commits on Jan 28, 2025

• Factorize thetaS and water supply. Remove some unused variables.

  

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• Remove unused

  

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  350f3b9

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• Simplify vegn tile

  

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Commits on Jan 29, 2025

• Minor refactoring

  

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• Simplify working with pools. Minor output changes

  

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• Simplify working with pools.

  

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Commits on Jan 30, 2025

• Minor refactoring: add pure qualifiers

  

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• Removed unused and error prone biomee interfaces.

  

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Commits on Jan 31, 2025

• Add output mappings

  

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• Refactoring class names and populate input interface using member procedure.

  

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• Minor refactoring

  

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Commits on Feb 3, 2025

• Minor refactoring: add comments

  

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• Update upload-artifact version to v4 (compulsory)

  

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