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LDNDC integration - update #3242

Merged
merged 73 commits into from
May 17, 2024
Merged

LDNDC integration - update #3242

merged 73 commits into from
May 17, 2024

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HenriKajasilta
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Description

A lot of changes compared to the earlier LDNDC push.

  • It is not anymore fixed to simulate only certain sites with specific inputs
  • Writes site and species parameters based on the given priors
  • Can use initial conditions from given source/path
  • Possible to simulate several grass and crop species
  • Writes outputs for LAI, several fluxes, soil moistures and biomasses
  • Expects that driver and event files are given in pecan.xml
  • Updated the documentation page, which has up-to-date situation of the model integration

Motivation and Context

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.
  • My name is in the list of CITATION.cff
  • 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.

@HenriKajasilta
Added new xml templates that write.configs.LDNDC will utilise and wri…
21f4cb5 
…te over
@HenriKajasilta
Added siteparameters and more species parameters that write.config.LD…
ead6324 
…NDC will try to read. In principle, additions will make the models simulations use more parameters, if available
@HenriKajasilta
Respirations read from the model output files, adds respirations and …
aa59d86 
…NEE to the netcdf files that will be written
@HenriKajasilta
Unnecessary files that have been replaced with templates are removed
582d804
@HenriKajasilta
Choose respiration variables from model output files that will be uti…
acf6124 
…lised when making the netcdf files
@HenriKajasilta
Filled in the airchemistry file with data representing measurements i…
fe7a23b 
…n Finland
@HenriKajasilta
Added groundwater option to the project template
5a02fef
@HenriKajasilta
Added groundwater data from Viikki site
1e01769
@HenriKajasilta
Keep data from all the simulated days instead of focusing only to the…
573bbea 
… growing season (or dates that physiology file prints)
@HenriKajasilta
Added new species and site parameters that are checked when writing t…
3b02497 
…he configurations. Writing configs changed to work for two specific site ids and writes the required files either for grassland or arable point of view based on that given site id.
@HenriKajasilta
Separated event and setup files for two different sites. This is temp…
5581d69 
…orary solution and later on events and setup files should be general and filled in while writing the configs based on the site properties
@HenriKajasilta
Events templated removed, because of the new events files created
014a71a
@HenriKajasilta
Setup template removed, because of the new setup files created
440ba29
@HenriKajasilta
Possibility to read soil files and write the info to the site templat…
e557baa 
…e. If no path soil file specified, use default values
@HenriKajasilta
Reconstructed the site template
d10cfba
@HenriKajasilta
Modified the events templates, so initial values can be places if needed
7ca1328
@HenriKajasilta
Changed the write.config file so that it can write the initial condit…
5b6ab44 
…ions from the given file paths. File site.template has been changed accordingly
@HenriKajasilta
Added sections in order to run forest simulations, changed the way to…
d024938 
… inform model about initial soil conditions
@HenriKajasilta
Added more dynamism to template
de3605e
@HenriKajasilta
Preparing the templates in order to make the workflow of running the …
fa3d0d3 
…model more general
@HenriKajasilta
Small fixes to setup files and way to handle them
218f458
@HenriKajasilta
Deleted site specific setup files, this in now handled in write.confi…
46717ee 
…gs.R
@HenriKajasilta
Template for events, when reading the management information from jso…
d121efe 
…n. This is a plain test version
@HenriKajasilta
Started drafting on how to read management information for the model,…
070939b 
… if it is given as a json -format
@HenriKajasilta
Changed template so that the physiology model has options
8e5d840
@HenriKajasilta
Adding speciesparameters is now more straight-forward in arable simul…
1377691 
…ations
@HenriKajasilta
Adds global time on top of climate file when it is prepared
6bfd32b
@HenriKajasilta
Removed extra dashes when preparing site file
f09363b
@HenriKajasilta
Take into an account, if there are multiple crops growing at the same…
30d91d1 
… time, this will change how the data is presented in physiology output
@HenriKajasilta
Simplifying the structure of writing configurations, changing it to n…
034a9ec 
…ot be site specific but that it would work more generally based on the given pfts
@mdietze
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mdietze commented Feb 25, 2024

@HenriKajasilta @istfer wanted to ping y'all about finishing up this PR

infotroph
infotroph reviewed Feb 27, 2024
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@mdietze mdietze added this pull request to the merge queue May 17, 2024
Merged via the queue into PecanProject:develop with commit c28158b May 17, 2024
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@infotroph infotroph infotroph left review comments

@istfer istfer istfer left review comments

@mdietze mdietze mdietze approved these changes

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4 participants
@HenriKajasilta @mdietze @infotroph @istfer