Skip to contents

Changelog

Source: NEWS.md

PEcAn.SIPNET 1.10.0

Added

  • write.events.SIPNET() generates SIPNET events.in files from an events.json file (#3623).
  • met2model.SIPNET now accepts argument var.names, listing which variables should be extracted from the file. If not provided, it extracts all variables in the file (#3563).

Removed

  • The sipnet2datetime function is no longer used anywhere and therefore has been removed (#3622).

Changed

  • Breaking: Renamed the setting used to pass soil and hydrology parameters. write.config.SIPNET previously read these from settings$run$inputs$soilinitcond, now settings$run$inputs$soil_physics to better reflect that these are state factors applicable to the whole run rather than initial conditions (Quianyu Li, #3406).
  • model2netcdf.SIPNET no longer writes separate <year>.nc.var files for every year of output. Use PEcAn.utils::nc_write_varfiles() to create these as needed (#3611).
  • Restart and met2model functions now print less to the console unless verbose = TRUE (#3544, #3563).

Fixed

  • write.config.SIPNET now checks more carefully whether an optional variable exists in an initial condition file before trying to read it, therefore printing fewer messages about (expectedly) missing variables (#3545).
  • When passed a vector of multiple input paths, write.config.SIPNET was choosing one at random; it now throws an error (Blesson Thomas, #3298). Note that a single input path per call has always been the intended usage; being passed many was a second bug in PEcAn.uncertainty that is also now fixed.
  • model2netcdf.SIPNET no longer assumes a constant value of pecan_start_doy across years, which lead to incorrect calculations of sub_dates and sub_dates_cf at year boundaries (@DongchenZ, #3622).
  • When phenology inputs contain missing values, write.config.SIPNET now tries to use an average across years for that site before falling back to fixed cross-site defaults (Quianyu Li, #3680).
  • write.config.SIPNET now adjusts soil water capacity to match the specified soil depth (#3634).
  • Fixed unit errors in write.config.SIPNET calculation of leafCSpWt and Amax (#3608, #3664).

PEcAn.SIPNET 1.9.0

License change

  • PEcAn.SIPNET is now distributed under the BSD three-clause license instead of the NCSA Open Source license.

Fixed

  • met2model.SIPNET() now stops with an error if the result contains missing values, which are not allowed in SIPNET inputs (#3474).
  • write.config.SIPNET() now consults PFT trait definitions to decide whether to initialize LAI in the leaf-on or leaf-off state, instead of the previous hard-coded defaults (#3419). Specifically:
    • a PFT with fracLeafFall > 0.5 will be treated as deciduous (previously hardcoded to deciduous for anything other than boreal conifers)
    • deciduous PFTs will get laiInit=0 if the simulation start date is not between leafOnDay and leafOffDay (previously hardcoded to May through September)
  • The generated Sipnet run script (job.sh) now works correctly, including across machines, when met/input/output files are specified relative to the working directory (#3418). Absolute paths continue to work as always.

PEcAn.SIPNET 1.8.0

  • Support for all Sipnet variables in read_restart and write_restart, for integration with state data assimilation workflows

PEcAn.SIPNET 1.7.1