Updated README with a more complete model description and instructions for installing SIPNET (#3705)
Removed tests/Rcheck_reference.log, which was used to ignore historic check messages that have now been fixed.
Initial support for SIPNET v2.0, whose features include simplified input files, simulation of management events, tracking of N cycle components, and anaerobic CH4 generation.
Breaking: met2model.SIPNET now writes 12-column clim files (as expected by Sipnet >= v2.0) by default. To get the previously standard 14-column output, set clim_format_version = "v1".
NITROGEN_CYCLE, LITTER_POOL, and ANAEROBIC enabled by default for SIPNET v2 runs.
model2netcdf.SIPNET now handles both V1 and v2 output header format (v2 has no Notes line; SIPNET #267).
Removed 13 obsolete v1 parameters from the v2 parameter template template.param_v2 (microbeInit, qualityLeaf, etc.) and added 16 new nitrogen cycle, anaerobic, and methane parameters.
Added nitrogen cycle (mineral_N, soil_organic_N, litter_N, N2O, N leaching, N fixation, N uptake) and methane (CH4) output conversion to NetCDF in model2netcdf.SIPNET.
Fixed crash when litterWater column absent in v2 output (LITTER_WATER removed in v2).
write.config.SIPNET now validates runtime flag dependencies (NITROGEN_CYCLE requires LITTER_POOL and ANAEROBIC) and guards v1 only parameters (litterWHC, litWaterDrainRate, litterWFracInit, microbeInit, m_ballBerry) from being set when using v2 templates.
Removed workarounds for column naming bugs in output from long-outdated legacy Sipnet version sipnet.unk.
Added trait to parameter mappings for 13 nitrogen cycle parameters in write.config.SIPNET, including tissue C:N ratios, N volatilization/leaching, fixation, and methane rates.
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.
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