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Dynamic roots md bugfix rkupdates #2

Merged
merged 232 commits into from
Oct 7, 2021
Merged

Dynamic roots md bugfix rkupdates #2

merged 232 commits into from
Oct 7, 2021

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rgknox
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@rgknox rgknox commented Oct 4, 2021

This PR:

  1. merges in master
  2. encapsulates rooting depth in a routine
  3. adds rooting depth to bisection routine
  4. double checked and addressed what to do with non-rooted layers

rosiealice added 30 commits April 30, 2020 02:22
@rosiealice
roll back snow burial change
d9f2ca0
@rosiealice
initial set of nocomp changes. doesn't work yet
3fc6a94
@rosiealice
phase 2 of nocomp mods
a08cbcd
@rosiealice
first pass through spawn_patches
3f92ed8
@rosiealice
added initialization mods
db960fd
@rosiealice
debug in EPD. will need rolling back
782b61a
@rosiealice
init fixes. gets out of init loop
ff0cf19
@rosiealice
rolling back changes in EDPatchdynamics to allow debugging of EDInit …
92f547a 
…first
@rosiealice
this version of edinit works. committing before cleaning up
ca1a60b
@rosiealice
modify number of patches and patch initialization
ed08bf1
@rosiealice
make disturbance arrays in EPD
8ed597a
@rosiealice
modifications to spawn patches for PFT array disturbance
7e77c3d
@rosiealice
modifications to terminate_patches for PFT loops
b48de6a
@rosiealice
reformatting the PFT loop in spawn patches
8e8e91f
@rosiealice
removing write statements from EDInit
2b08a8d
@rosiealice
fixing issues with area in spawn patches2667
30659c9
@rosiealice
fixed references to currentPatch in terminate patches
02db378
@rosiealice
added olderp ref to cp loop in terminate patches
34f3532
@rosiealice
located error in the small size tolerances. Eraase <1% patches to fix
ce71fda
@rosiealice
added filter to init cohorts
9ad82a7
@rosiealice
fixed memory leak. removed write statements
ba0aca6
@rosiealice
changes to make one pft per patch
7dda68f
@rosiealice
turning off patch dynamics allows nocomp to run
5dcef9f
@rosiealice
fixing error in spawn_patches
1e1f013
@rosiealice
initial go at converstion matrix. Hard wired, e dimensional
630d571
@rosiealice
fixing patch dynamics bug in EDmain
1e4d30c
@rosiealice
fixing erroneous error check
2ee7316
@rosiealice
2D pft mapping array
aa620f9
@rosiealice
implement new hlm_pft_map 2D parameter
a69ac89
@rosiealice
adding usage of hlm_pft_map
6927dec
rgknox and others added 28 commits August 9, 2021 17:36
@rgknox
Updated notes on the bci patch xml file to include Koven et al. 2019
e065f7f
@glemieux
manually reverting diagnostic writes
9e646dc
@glemieux
removing more diagnostics
d94ca1a
@glemieux
refactoring the linked list for zero patch area with nocomp
ec99726
@glemieux
Slight refactoring ed_ecosystems_dynamics for simplicity
5111220 
Refactored the do_patch_dynamics check added for SP mode as well
as some older duplicate logic checks that can be combined.
@glemieux
reverting all the area_pft indexing commits
443550d
@glemieux @ckoven
Update biogeochem/EDPhysiologyMod.F90
28473d0 
Updating the element id from a number to the element parameter name to clarify.

Co-authored-by: Charlie Koven <ckoven@users.noreply.github.com>
@glemieux
Merge branch 'fates_sp_sept_revert_area_pft' into fates_sp_sept
1341f4b
@ckoven
adding hist var for sp lai by pft
a260f31
@ckoven
removing init and c_leaf arguments to assign_cohort_SP_properties
455617d
@ckoven
Revert "removing init and c_leaf arguments to assign_cohort_SP_proper…
919e27f 
…ties"

This reverts commit 455617d.
@ckoven
changing area_pft indexing in init
5664f68
@ckoven
debug
482fc94
@ckoven
fixing loop bounds
d2892e4
@ckoven
indexing bc_outs to ignore the bare-groun PFTs entirely.
c009135
@ckoven
Revert "adding hist var for sp lai by pft"
3507ad3 
This reverts commit a260f31.
@ckoven
bugfixes
70c3195
@ckoven
added fire variables to allow nocomp to pass restart comparison with …
cc5b2ed 
…fire on
@glemieux
Merge pull request #7 from ckoven/spmode_firerestdebug
5f88d09 
new fire restart variables
@glemieux
correcting the location of the ncl cohort index assignment
54e35d1
@glemieux
Merge pull request NGEET#703 from rosiealice/fates_sp_sept
f32d831 
Fates SP mode
@rgknox
Conflict resolution on batch patch modifications to ../tools/modify_f…
70917d4 
…ates_paramfile.py.
@rgknox
Merge pull request NGEET#765 from rgknox/mod-e3sm-testparam
70a3e13 
batch script for generating parameter file from a diff file
@rgknox
Removed unnecessary manual attribution statement (author history in g…
b7fd5f5 
…ithub)
@rgknox
Merge resolution of rooting depth with master. Unification of crown d…
f7aa5b1 
…epth function usage
@rgknox
Small fix in batch params script to workaround parser bug
a7b29b4
@rgknox
cleaning up root depth branch
a3b094f
@rgknox
Created subroutine for maximum rooting depth, passing that into root …
c944640 
…bisection method used for getting transporting root depth
@JunyanDing JunyanDing merged commit f0802ed into JunyanDing:DynamicRoots_MD_bugfix Oct 7, 2021
@rgknox rgknox deleted the DynamicRoots_MD_bugfix_rkupdates branch October 31, 2023 17:55
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5 participants
@rgknox @JunyanDing @rosiealice @ckoven @glemieux