Dev merge eclm with FruitTree and WinterCrops all at once

[AGonzalezNicolas]

PULL REQUEST info

This pull request wants to include the following developments:

• Fruit Tree (FT) from @odombro (repo, publication)
• Winter Crops (WC) from @tboas (tboas/CTSM@0b38504, publication)

Into the last eclm-commit a72229c of repo HPSCTerrSys/eCLM/ by merging branch-eclm of repo HPSCTerrSys/clm5_0. Below there is a detailed explanation how branch-eclm of repo HPSCTerrSys/clm5_0 is produced.

Before accepting this pull request, the following needs to be checked:

• build works
• run Wüstebach case with fields-names adapted to FT and WC (otherwise will fail)
• check results Wüstebach case agains reference Wüstebach results
• run FT
• check results FT against reference FT results
• run WC
• check results WC agains reference WC results

Next steps should include to run these 3 cases in CI.
This should conclude issues: #94, #93, #45

This only can be done with scientific support from IBG-3 (e.g., @tboas, @Toeroeoe).

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STEPS FOLLOWED TO MERGE FT and WC into clm5.0:

1. Start two new dev-branches with the most updated clm5.0 version at that moment (commit e7285f6caeec6f0b35b25a6d49cb59f41d1a0c3e) in our HPSCTerrSys/clm5 repo

2. Merge WC (tags/reelase_08_2020) development with one of the new dev-branches --> release-clm5.0_WinterCrops

   • There was only one conflict: README file.
   • Merged branch with WC release-clm5.0_WinterCrops.

3. Merge FT with the other new dev-branch --> release-clm5.0_FruitTree

   • There was only one conflict: README file.
   • Merged branch with FT release-clm5.0_FruitTree.

4. Replace variable names on FT branch --> release-clm5.0_FruitTree_namesVar

   • The nomenclature used in release-clm5.0_WinterCrops was different from release-clm5.0_FruitTree. release-clm5.0_WinterCrops used variables as covercrop_1 and covercrop_2.
   • To support the merge of FT and WC, @tboas, @odombro, and @AGonzalezNicolas agreed to replace the following variable names within therelease-clm5.0_FruitTree:

Old name	New name	Comments
tropical_soybean	covercrop_1	Made by @tboas in WinterCrops, Add to FruitTree branch
irrigated_tropical_soybean	covercrop_2	Made by @tboas in WinterCrops, Add to FruitTree branch
ncitrus	napple	Add to FruitTree branch
nirrig_citrus	nirrig_apple	Add to FruitTree branch

These variable replacements are found in this other branch release-clm5.0_FruitTree_namesVar.

5. Merge WC-branch into FT_new_variable_names --> release-clm5.0_FTWC

• There were several conflicts:

README
src/biogeochem/CNPhenologyMod.F90
src/biogeochem/CropType.F90
src/biogeochem/NutrientCompetitionFlexibleCNMod.F90

I used Visual studio code to manually solve conflicts one by one (no agents, no AI involved).

The branch with both merged developments is clm5_FTWC.

6. Check results with references after merge

• FruitTree versus merged clm5_FTWC --> No differences
  Case files here

• WinterCrops versus merged clm5_FTWC --> No differences
  Case files here

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Once the merge is considered successful (after validation against the reference cases), I proceeded to change structure of clm5 to eclm while preserving the commit history of clm5.

STEPS FOLLOWED from clm5-structure to eclm-structure

1. Starting point is branch release-clm5.0_FTWC of repo HPSCTerrSys/clm5_0.
2. Change structure of repository to be similar to eclm-structure (HPSCTerrSys/eclm repo)

• Work on dev-branch based on release-clm5.0_FTWC --> eclm_base_00
• Apply bootstrap_v2_FTWC_00 --> very similar to what @kvrigor had applied to fork eclm
• Apply git-filter-repo --> to preserve clm5 commit history

3. Merge eclm_base_00 with eclm first commit (f6b981f) by applying:

git merge f6b981fe617dde16f8e7d814b98d12312c8f823c --allow-unrelated-histories

And solve conflicts on Viscual Code Studio manually.

4. Add commits from the HPSCTerrSys/eCLM repo one by one
   • This resulted in the branch-eclm of the HPSCTerrSys/clm5_0 repo.
   • Last commit added to this eclm-branch was commit b882524 from the HPSCTerrSys/eCLM repo.