rsofun - rsofun 5.1.0

New features

• P-model:

  • New run_pmodel_onestep_f_bysite() adds single-step leaf-level simulations
    of the P-model
  • Changed temperature dependencies of Vcmax and Jmax (see breaking changes below)
  • Added support for carbon isotope tracking
    • run_pmodel_onestep_f_bysite() returns bigdelta, i.e. the carbon
      fractionation of fresh assimilate cleafd13c relative to d13c_atm,
      thereby avoiding any assumptions for d13c_atm.
    • run_pmodel_f_bysite() and runread_pmodel() newly return cleaf and cleafd13c,
      assuming a constant atmospheric signature d13c_atm = -8.4 permil. In a future
      version daily values of d13c_atm could/should be included in the input forcing.

• BiomeE:

  • Added support for LULUC (land use, land-use change) in BiomeE. See vignette
    biome_luluc for details.
  • New BiomeE behavior to recycle last year of forcing if requested simulation
    time span (nyeartrend) is longer than available forcing data.
  • Prepared support for carbon isotope tracking
    • run_biomee_f_bysite() and runread_biomee() do track carbon isotopes internally,
      currently without output. Note that when method_photosynth == "gs_leuning", then
      bigdelta = 20, whereas when method_photosynth == "pmodel" then bigdelta is
      computed based on the pmodel-derived chi.

• calib_sofun() now passes parameters as a named vector to cost-functions for
  easier processing within cost-functions. Default cost-functions were updated,
  but currently ignore the names. This is fully backward compatible, but allows
  to use the names in user-created cost functions.

Breaking changes

• P-model now computes temperature dependencies of jmax and vcmax
  with Kumarathunge et al. (2019) instead of Kattge & Knorr (2007), effectively
  using a dampened signal for tc_growth and long-term averages for tc_home. This
  alters the simulation results. Formatting of inputs remains unchanged.

• Breaking changes in BiomeE drivers:

  • init_cohort$init_n_cohorts column has been phased out and must not be present in
    drivers to protect against data corruption.
  • update_annualLAImax flag was removed and the behavior is now slightly altered
    since LAImax and underLAImax are set and kept constant at the start of the simulation:
    • LAImax takes value max(LAI_light, 0.5)
    • underLAImax takes value min(LAImax, 1.2)
  • do_closedN_run flag now uses initial inorganic N setting rather than arbitrary value
    and is false by default.
  • Modified drivers to use more sensibles values
    • Species 1 is now a C4 crop
    • N_input is set to 0.01 to limit N starvation.

• Breaking changes in BiomeE output

  • renamed the following column names in output_daily_tile:
    • totWs=>SoilWater
    • Trsp=>Transp
    • SW_C=>sapwoodC and SW_N=>sapwoodN
    • HW_C=>heartwoodC and HW_N=>heartwoodN
    • McrbC=>mcrbC and McrbN=>mcrbN
    • added NPP
  • renamed the following column names in output_annual_tile and output_annual_cell:
    • rain=>Prcp
    • SeedC=>seedC (and for N)
    • SapwoodC=>sapwoodC (and for N)
    • WoodC=>heartwoodC (and for N)
    • SlowSOM=>slowSOM
    • McrbC=>mcrbC and McrbN=>mcrbN
    • added totC
  • renamed the following column names in output_annual_cohorts:
    • nsc=>NSC and nsn=>NSN
    • sapwC=>sapwoodC
    • woodC=>heartwoodC
    • Nupt=>N_uptk
    • Nfix=>N_fxed
    • switched column positions of NPP and GPP

Biosphere - Plants and Vegetation - Fortran
Published by fabern 8 months ago

rsofun - v5.0.1

• This model version behaves exactly as the version before.
• Version update was necessary to deposit a copy on Zenodo that includes improved description of scripts and data used for the model documentation paper (Paredes et al.)

Biosphere - Plants and Vegetation - Fortran
Published by fabern about 1 year ago

rsofun - v5.0.0

CRAN release

This release is available on CRAN.

What's Changed

• Major stability improvements of BiomeE (fix segmentation faults and random outputs in the Fortran layer)
• Fix compilation to support all major platforms (LTO, parallel make, removed non supported language features)
• Removed prescribed net radiation option
• BiomeE and P-model forcing homogenization
  • prec is now called rain
  • rh is now provided as vpd
• Dynamic sized arrays are now supported (arrays passed along with their size to Fortran)

Full Changelog: https://github.com/geco-bern/rsofun/compare/v4.4...v5.0

Biosphere - Plants and Vegetation - Fortran
Published by marcadella over 1 year ago

rsofun - rsofun v4.4

This is the first CRAN release of the package. The changes introduced after previous releases are:

• Bugfix on input data type P-model
• LM3-PPA to BiomeE renaming
• Cost function rewrite
• Update output format (consistency)
• Add water balance variables to P-model output
• New p-model calibratable parameters
• Rewrite of temperature and soil moisture stress functions
• Update simulation parameters to take netrad, ppfd and ccov as input forcing
• Documentation parameter sensitivity analysis
• Documentation on the data format
• Document calibration diagnostic and model uncertainty calculation
• More transparent licensing and copyright statements in COPYING file

Biosphere - Plants and Vegetation - Fortran
Published by pepaaran over 2 years ago

rsofun - rsofun v4.4

This is the first CRAN release of the package. The changes introduced after previous releases are:

• Bugfix on input data type P-model
• LM3-PPA to BiomeE renaming
• Cost function rewrite
• Update output format (consistency)
• Add water balance variables to P-model output
• New p-model calibratable parameters
• Rewrite of temperature and soil moisture stress functions
• Update simulation parameters to take netrad, ppfd and ccov as input forcing
• Documentation parameter sensitivity analysis
• Documentation on the data format
• Document calibration diagnostic and model uncertainty calculation
• More transparent licensing and copyright statements in COPYING file

Biosphere - Plants and Vegetation - Fortran
Published by pepaaran over 2 years ago

rsofun - rsofun v4.3

Release version 4.3 jumps from 4.0 and includes substantial changes. Please check dependencies in you code if rerunning with version 4.3.

The list of changes include:

• catching aborting in FORTRAN part to avoid R session crashes (v4.1)
• canopy transfer solved for LM3-PPA with P-model (v4.2)
• general bugfixes (v4.2)
• consistent variable names p-model / lm3-ppa (v4.3)
• optimization stability BayesianTools (v4.3)
• new documentation (v4.3)

Biosphere - Plants and Vegetation - Fortran
Published by khufkens about 4 years ago

rsofun - rsofun v4.0

Public release after refactored code.

Biosphere - Plants and Vegetation - Fortran
Published by stineb over 4 years ago

rsofun - LM3-PPA implemented

LM3-PPA is now fully implemented in the master branch. Successfully compiles and runs both P-model and LM3-PPA simulations.

Unresolved bug:

• Crashes during runtime when compiled and run on one machine, but not on another. The problem concerns the tile-level output arrays output_daily_tile and output_annual_tile.

Biosphere - Plants and Vegetation - Fortran
Published by stineb about 6 years ago

rsofun - Data ingestion done outside.

Data ingestion now done outside rsofun (using ingestr package). Example complete in vignettes/example.Rmd.

Biosphere - Plants and Vegetation - Fortran
Published by stineb about 6 years ago

rsofun - v1.0.wrap_sofun

Version of rsofun used for Stocker et al. (2020) GMD. Wraps the SOFUN model (separate repository!) though input/output writing via files. No direct wrapping of the FORTRAN code within the rsofun package is implemented at this release.

Biosphere - Plants and Vegetation - Fortran
Published by stineb over 6 years ago

rsofun - Shared memory with Fortran

Biosphere - Plants and Vegetation - Fortran
Published by stineb over 6 years ago

rsofun - Version for eval_pmodel

This is the code version used for the eval_pmodel model documentation paper, and before Nick Smith's optimal Vcmax calculation is implemented (as optional method) and before pressure-dependence of $\Gamma^{\ast}$ and Michaelis-Menten-K parameters are implemented (as new standard).

Biosphere - Plants and Vegetation - Fortran
Published by stineb over 7 years ago