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{WIP} LPJ-GUESS SDA Couplers #2660

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{WIP} LPJ-GUESS SDA Couplers #2660

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istfer
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@istfer istfer commented Jul 17, 2020

Description

Here I am opening this PR as work in progress to publicly commit myself to it (some pun intended).

Motivation and Context

Couplers for LPJ-GUESS to run PalEON-SDA.

Review Time Estimate

  • Immediately
  • Within one week
  • When possible

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

  • My change requires a change to the documentation.
  • I have updated the CHANGELOG.md.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • All new and existing tests passed.

istfer and others added 30 commits June 8, 2019 13:37
@istfer
started new read state function
84f3c25
@istfer
add helper function that locates function
1c96f7d
@istfer
add helper function that finds closing paranthesis
2747330
@istfer
add function that finds stream
0518d2c
@istfer
start reading
c8fc996
@istfer
first read
4ac6530
@istfer
extract typedef enums
6e92048
@istfer
read typedef enum
6d2bac5
@istfer
read Historic
4221e09
@istfer
read vector
d477ca7
@istfer
read vector with const int
b1bf79e
@istfer
read in parameters header too
7faffa8
@istfer
case fo seed
3921cc3
@istfer
ready to loop over stands
2f8bbda
@istfer
start looping over patches
b3b0025
@istfer
reading individual class
45970e5
@istfer
first pass at read individual
d6ef1ec
@istfer
finish individual
d58848d
@istfer
few more flexibility
3ab63d9
@istfer
read matrix
83b996b
@istfer
getting ready to read sompool
f66c54a
@istfer
catch one more case
4a6ea5a
@istfer
finished soil
1bb8b87
@istfer
adding more hardcoded constants for now
d84f80f
@istfer
getting ready to read fluxes
f9899dd
@istfer
finished patch
af59c40
@istfer
finished reading all - first pass
4e42c6c
@MagicForrest
Added allometry and allocation functions from LPJ-GUESS. Also summing…
94d304c 
… variables to a per-gridcells basis, and first start on updating the state.
@istfer
read meta.bin
cc3cceb
@MagicForrest
allocation() function now correctly included
b88b529
MagicForrest and others added 25 commits June 21, 2019 16:03
@MagicForrest
Mostly code tidying/documentation ahead of merging.
aae14e6
@istfer
Merge branch 'LPJGUESS_SDA' into LPJGUESS_SDA
2b4e6b9
@istfer
Merge pull request #2 from MagicForrest/LPJGUESS_SDA
09ea06e 
First merge of LPJ-GUESS state updating code
@istfer
modifying function for PalEON version
6fdb02b
@istfer
Merge branch 'LPJGUESS_SDA' of https://github.com/istfer/pecan into L…
e34ea19 
…PJGUESS_SDA
@istfer
read new PhotosynthesisResults
c86b1a3
@istfer
updates for the new model version, first pass finished
ecc6faf
@MagicForrest
Documented adjustBiomass() and cleaned the fucntion a little.
cb206bf
@istfer
start read_restart.LPJGUESS
3df3ec0
@istfer
LPJGUESS uses exact days and will require split inputs function
a0d938e
@istfer
backbone of read_restart
9f8e777
@MagicForrest
Added HEIGHT_MAX as an argument to over-ride the LPJ-GUESS 150m max h…
aa3acf5 
…eight.
@MagicForrest
Merge branch 'LPJGUESS_SDA' of github.com:MagicForrest/pecan into LPJ…
85c4a1f 
…GUESS_SDA
@istfer
start split inputs for LPJGUESS
49085a5
@istfer
number of individuals are back
90c4c07
@MagicForrest
Just coding style
a0572c0
@istfer
Merge branch 'LPJGUESS_SDA' into LPJGUESS_SDA
fa628db
@istfer
Merge pull request #3 from MagicForrest/LPJGUESS_SDA
4f60bce 
merge hackathon pr
@istfer
define state year
3adac8e
@istfer
Merge branch 'LPJGUESS_SDA' of https://github.com/istfer/pecan into L…
94da6de 
…PJGUESS_SDA
@istfer
add doc tags
14d05f6
@istfer
LPJGUESS package build
47a7c05
@istfer
no need for single quote
e6d5138
@istfer
Merge branch 'develop' of github.com:PecanProject/pecan into LPJGUESS…
2273bbd 
…_SDA
@istfer
Merge branch 'develop' of github.com:PecanProject/pecan into LPJGUESS…
0f94f65 
…_SDA
mdietze
mdietze approved these changes Jul 20, 2020
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models/lpjguess/R/read_state.R

###################################### READ STATE

library(stringr)
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probably shouldn't be here

models/lpjguess/R/split_inputs.LPJGUESS.R
@@ -0,0 +1,131 @@
## split LPJ-GUESS ncdf files into smaller time units to use in KF
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FYI, this bit isn't needed unless the model, like sipnet, gets it start/end date info from its met files

@robkooper robkooper marked this pull request as draft September 9, 2020 21:36
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This PR is stale because it has been open 365 days with no activity.

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@mdietze mdietze mdietze approved these changes

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4 participants
@istfer @mdietze @MagicForrest @infotroph