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NEWS

SOILWAT2 v8.1.0

  • This version produces similar but not identical simulation output as previously because of the following changes:

    • Small deviations arise from replacing all remaining variables of type float with type double (see commit 62237ae on 2024-July-30).
    • Saturated percolation is now limited which leads to different outcomes during periods of high infiltration (e.g., snowmelt) and during conditions of low hydraulic conductivity (e.g., frozen soils, sapric organic matter).
    • Depth of snowpack is now consistent with snowpack water content.
    • Surface temperature extremes are now less sensitive to high biomass, and average surface temperature is now more consistent with daily extremes.

  • The two modes of SOILWAT2 can now be compiled with the following flags:

    • make CPPFLAGS=-DSWTXT (or as previously make all) for txt-based
    • make CPPFLAGS=-DSWNC for nc-based SOILWAT2.

  • SOILWAT2 now ends gracefully with termination (SIGTERM) and interrupt (SIGINT, commonly CTRL+C on the keyboard) signals.

  • nc-based SOILWAT2 can now use a large variety of "netCDF" data sources as inputs (#389; @N1ckP3rsl3y, @dschlaep). The user identifies in "SW2_netCDF_input_variables.tsv" which input variables are provided by "netCDF" (and vary among simulation runs, i.e., sites or grid cells); remaining inputs are obtained from the same text files as in txt-based mode (and are constant among simulation runs).

  • "ncTestRuns" provide a new framework that comprehensively tests nc-based SOILWAT2 via the script "tools/check_ncTestRuns.sh" by creating, executing, and checking more than 40 test runs.

    • Comprehensive set of spatial configurations of simulation domains and input netCDFs (see "tests/ncTestRuns/data-raw/metadata_testRuns.csv")
    • Runs with daily inputs from external data sources including "Daymet", "gridMET", and "MACAv2METDATA" (if available)
    • One site/grid cell in the simulation domain is set up to correspond to the reference run (which, by default, is equivalent to "tests/example" in txt-based mode); output at that site/grid cell is compared against the reference output

  • Tests now require c++17 and utilize googletest v1.15.2 (issue #427).

  • SOILWAT2 can now represent the influence of soil organic matter on the soil water retention curve and the saturated hydraulic conductivity parameter (#397; @dschlaep). The implemented approach first determines organic matter properties for the soil layers assuming fibric peat characteristics at the soil surface and characteristics of sapric peat at a user-specified depth. Then, bulk soil parameters of the soil water retention curve are estimated as linear combinations of properties for the mineral soil component and of properties for the organic matter soil component using the proportion of organic matter in the bulk soil as weights. The bulk soil saturated hydraulic conductivity parameter accounts for flow pathways through organic matter above a threshold and assumes conductivities through mineral and organic components in series outside of those pathways.

  • Saturated percolation is now limited. The upper bound is a function based on the saturated hydraulic conductivity parameter (which includes effects of organic matter), frozen soils, and a user-specified "permeability" factor.

  • Fix the calculation of depth of snowpack (#441; @dschlaep). Depth of snowpack is now calculated after sublimation occurred and is based on snowpack density that now is always larger than 0; this now makes depth of snowpack and snowpack water content consistent.

  • Fix the estimation of surface temperature (#440; @dschlaep). Biomass effects are now capped at a value at which cooling and heating effects on minimum and maximum surface temperature result, across average conditions, in no change for mean surface temperature. Effects of maximum air temperature on maximum surface temperature are limited to air temperatures above freezing. Minimum and maximum surface temperature are now set to their average (with a warning) if the initial estimate of minimum surface temperature is larger than the initial estimate of maximum surface temperature. Average surface temperature is now (by default) estimated from minimum and maximum surface temperature (instead of independently as previously), but the old method can be selected.

Changes to inputs

  • New input via "siteparam.in" to specify the depth at which characteristics of organic matter have completely switched from fibric to sapric peat (default is 50 cm).
  • New input via "siteparam.in" to select the method for estimating surface temperature (with a new default).
  • New input via "soils.in" to provide the proportion of soil organic matter to bulk soil by weight for each soil layer.
  • New input via "swrc_params*.in" to provide parameter values of the soil water retention curve representing fibric and sapric peat. Note: Some parameter values for the "FXW" SWRC are missing.
  • "climate.in": new snow density values for July, August and September estimated with linear interpolation from June and October values.
  • New command line option "-p" to prepare the domain/progress, index, and output files; with this flag, no simulations will be run.

Changes to inputs for nc-based SOILWAT2

  • New tab-separated value "tsv" input file "SW2_netCDF_input_variables.tsv" that lists, activates, and describes each input from "netCDF" files. This file replaces "files_nc.in".
  • "desc_nc.in" provides new inputs for the names of geographic and projected "CRS" variables as well as names for the spatial coordinate axes and variables.
  • New example inputs as "netCDF" files that exactly txt-based inputs
    • "inClimate/monthlyClimate.nc" corresponding to "climate.in"
    • "inSoil/soil.nc" and "inSoil/swrcp.nc" corresponding to "soils.in" and "swrc_params.in"
    • "inTopo/topo.nc" corresponding to "modelrun.in"
    • "inVeg/veg2.nc" and "inVeg/vegPFT.nc" corresponding to "veg.in"
    • "inWeather/weather.nc" corresponding to "data_weather/weath.*"

SOILWAT2 v8.0.1

  • Simulation output remains the same as the previous version unless relative humidity is calculated from vapor pressure or specific humidity.

  • Fix the calculation of relative humidity (#435; @dschlaep). Previously, relative humidity was incorrectly calculated if based on vapor pressure or specific humidity. The calculation of relative humidity from specific humidity now also uses elevation (to estimate air pressure).

  • Fix the count of days on which a missing weather value was replaced by a non-missing value from the preceding day for the method "LOCF" (last observation carried forward; #437; @dschlaep). Previously, any day with a missing weather value was counted.

Changes to inputs

  • Units of specific humidity inputs changed from "%" to "g kg-1".

SOILWAT2 v8.0.0

  • Simulation output remains the same as the previous version. However, output of establishment/recruitment for two species is now generated by default by the example simulation run.

  • SOILWAT2 can now be compiled in one of two modes: "nc" and "text" (#361, #362, #363; @N1ckP3rsl3y, @dschlaep):

    • "nc"-based SOILWAT2: output files are produced in "netCDF" format; input files in "netCDF" format are currently limited to the "domain". This mode is compiled if the new preprocessor definition "SWNETCDF" and the "netCDF-c" library are available, e.g., make CPPFLAGS=-DSWNETCDF all
    • "text"-based SOILWAT2 (as previously): output files are plain text that are formatted as comma-separated values "csv"; input files are plain text.

  • SOILWAT2 now represents a simulation "domain", i.e., a set of (independent) simulation units/runs (#360; @N1ckP3rsl3y, @dschlaep). A "domain" is defined by either a set of "sites" or by a "xy"-grid. The current simulation set consists of simulation units within a "domain" that have not yet been simulated. Simulation units are identified via "suid" (simulation unit identifier).

    • Input text files are read once and now populate a "template" that is used for each simulation unit.
    • New SW_CTL_RunSimSet() loops over the simulation set or runs one user specified simulation unit. It writes warning and error messages from all simulation units to the logfile but does not exit if a simulation unit fails (main() will exit with an error if it fails or if every simulation unit produced an error).
    • New SW_CTL_run_sw() takes a deep copy of the "template" as basis for each simulation unit.
    • For "netCDF"-based SOILWAT2, information about the "domain" (i.e., simulation units and their geographic locations) is obtained from "domain.nc" (#361; @N1ckP3rsl3y, @dschlaep).
    • For "nc"-based SOILWAT2, simulation progress (success/failure) is tracked by "progress.nc" (#387; @N1ckP3rsl3y, @dschlaep); progress tracking makes re-starts after partial completion of the simulation set by an earlier execution possible.

  • SOILWAT2 can now be compiled with "udunits2" to convert output to user requested units (#392; @dschlaep, @N1ckP3rsl3y).

    • Unit conversion is available only in "nc"-mode and if compiled with the new preprocessor definition "SWUDUNITS" and if the "udunits2" library is available, e.g., make CPPFLAGS='-DSWNETCDF -DSWUDUNITS' all.
    • Users request output units via field "netCDF units" of the input file "SW2_netCDF_output_variables.tsv".

  • Tests now utilize the same template/deep-copy approach (@dschlaep), i.e., input files from test/example/ populate a "template" and test fixture deep copy the "template" (avoiding repeated reading from disk).

  • SOILWAT2 gained basic time tracking and reporting (#380; @dschlaep). Temporal resolution may only be full seconds (for C99) but could be sub-seconds (for C11 or later). The runs over the simulation set end gracefully if a user specified wall time limit is (nearly) reached (nearly is defined by SW_WRAPUPTIME). A report is written to stdout or (silently) to the logfile if user requested quiet mode; the report includes

    • Overall wall time and proportion of wall time for the simulation set
    • Time of simulation units and reports average, standard deviation minimum and maximum time.

  • SOILWAT2 gained spin-up functionality (#379; @niteflyunicorns, @dschlaep). A user-requested sequence of (random) years is simulated (without output) before the actual simulation run to provide better starting values (e.g., soil moisture, soil temperature). User inputs are obtained from "domain.in".

  • The random number generator "pcg" is now a submodule of a forked copy of the previous repository imneme/pcg-c-basic (#353; @dschlaep). This allowed us to fix a function declaration without a prototype.

  • Specified a consistent code style and formatted code, header include directives, doxygen documentation, and updated code contribution guidelines (#316; @dschlaep).

Changes to inputs

  • New input file "domain.in" with input variables that specify type and spatial dimensions of the simulation "domain" (with a backwards compatible default of one site), start and end year (the latter previously in "years.in"), and spin-up information (mode, duration, scope). This input file uses a key-value pair approach, i.e., inputs must use the correct key while they don't have to be on a specific line (as they have to be in other input files).
  • Input file "years.in" was removed (content moved to "domain.in").
  • New input file "modelrun.in" with inputs for geographic coordinates and topography (previously in "siteparam.in").
  • Input file "siteparam.in" lost inputs for geographic coordinates and topography (content moved to "modelrun.in").
  • Input file "files.in" gained two entries for "nc"-based SOILWAT2.
  • New command line option "-s X" where X is a simulation unit identifier; if the option "-s X" is absent or X is 0, then all simulation units in the simulation "domain" are run; otherwise, only the simulation unit X is run.
  • New command line option "-t X" where X is the wall time limit in seconds. The code gracefully ends early if the wall time reaches a limit of X - SW_WRAPUPTIME seconds; if the option "-t X" is absent, then there is (practically) no wall time limit.
  • New command line option "-r" to rename netCDF domain template file to domain file name provided in "Input_nc/files_nc.in".

Changes to outputs

  • Output of establishment/recruitment for two species is now generated by default by the example simulation run (#411; @dschlaep).

Changes to inputs and outputs for "nc"-based SOILWAT2

  • "nc"-based SOILWAT2 is compiled if the new preprocessor definition "SWNETCDF" is available, e.g., make CPPFLAGS=-DSWNETCDF all; the capability to convert units is compiled with the new preprocessor definition "SWUDUNITS", e.g., make CPPFLAGS='-DSWNETCDF -DSWUDUNITS' all
  • User-specified paths to external headers and libraries can be provided
    • "netCDF-c" headers: NC_CFLAGS="-I/path/to/include"
    • "netCDF-c" library: NC_LIBS="-I/path/to/lib"
    • "udunits2" headers: UD_CFLAGS="-I/path/to/include"
    • "udunits2" library: UD_LIBS="-I/path/to/lib"
    • "expat" headers: EX_CFLAGS="-I/path/to/include"
    • "expat" library: EX_LIBS="-I/path/to/lib"
  • New input directory "Input_nc/" that describes "nc"-based inputs (paths provided by new entries in "files.in").
  • New text input file "files_nc.in" that lists for each input purpose (currently, "domain" and "progress" are implemented) the path to the "netCDF" input file and associated variable name.
  • New text input file "attribues_nc.in" to provide global attributes and a geographic (and optionally a projected) "CRS" (coordinate reference system) that describe the "domain.nc".
  • A user provided "domain.nc" that describes the simulation "domain". Specifications must be consistent with "domain.in". If absent, a template is automatically generated based on "domain.in".
  • A user provided "progress.nc" that describes the simulation "progress". Specifications must be consistent with "domain.nc". The "progress" variable can optionally be contained in "domain.nc" instead of a separate file. If absent, it is automatically generated based on "domain.nc".
  • New tab-separated value "tsv" input file "SW2_netCDF_output_variables.tsv" that lists, activates, and describes each output variable in "netCDF" mode.
  • All outputs are written to "netCDF" files based on user requests from "SW2_netCDF_output_variables.tsv". Each "netCDF" output file contains the output variables from one output group "outkey" and one output period (daily, weekly, monthly, yearly).

SOILWAT2 v7.2.0

  • Simulation output remains the same as the previous version.

  • SOILWAT2 now handles errors more gracefully (#346; @N1ckP3rsl3y, @dschlaep).

    • Code no longer crashes on error immediately (except for STEPWAT2).
    • Code stores messages of warnings and error status.
    • All functions now check for errors and return early (after cleaning up memory).

  • SOILWAT2 now defines its own structure for random numbers (#373; @dschlaep). This allows to hide implementation details, i.e., STEPWAT2 will no longer need to interact directly with pcg and rSOILWAT2 will no longer depend on pcg which it never has used.

  • New sw_strtok() is thread-safe and replaces not thread-safe strtok() (#376; @N1ckP3rsl3y).

  • Obsolete code in DEBUG_MEM* sections is removed (#369; @dschlaep).

SOILWAT2 v7.1.0

  • Simulation output remains the same as the previous version.

  • Prepare for SOILWAT2 to become thread-safe and reentrant (#346; @N1ckP3rsl3y, @dschlaep)

    • Definition clarifications
      • Thread-safe - Multiple threads (a future SOILWAT2 development) will not influence each other unintentionally. Here, we implemented structures to enable thread-local storage, i.e., each thread operates on local data structures or with static data.
      • Reentrant - The ability to correctly execute any part of the program by multiple threads simultaneously but independently from others.
    • All non-static variables are replaced by local variables; functions gained arguments to pass local variables by reference (replacing global variables).
    • New main abstract types
      • SW_ALL - Contains the existing structures that are relevant for the simulation itself, e.g., SW_MODEL, SW_SOILWAT, SW_WEATHER.
      • PATH_INFO - Holds information about location of input and output data, e.g., directories, file paths to input data.
      • SW_OUTPUT_POINTERS - Points to requested output subroutines.
      • LOG_INFO - Manages information for logging warnings and errors.

  • Tests now require c++14 and utilize googletest v1.14.0 (issue #339).

  • Bugfixes

    • Fix an error where a pointer was freed even though it was not allocated (issue #356; @dschlaep).
    • Fix memory leak in test of SW_VPD_construct() (issue #205; @dschlaep).

Changes to inputs

  • The output separator OUTSEP has been unused since the switch (v4.0.0) from writing free-form text files to "csv" spreadsheets (where the separator is fixed to a comma); the occurrence of OUTSEP in "outsetup.in" is now deprecated and triggers a warning.

SOILWAT2 v7.0.0

  • This version produces nearly identical simulation output as the previous release under default values for the new inputs. Small deviations arise due to a fix in the handling of soil moisture values when between field capacity and saturation.

  • Multiple soil water release curves (SWRC) are now implemented and can be selected with new input swrc_name. Implemented SWRCs currently include "Campbell1974", "vanGenuchten1980", and "FXW". New input has_swrcp determines if parameters for a SWRC are estimated at run-time via an implemented pedotransfer function (PTF) based on new input ptf_name or if they are provided as inputs via new input file "swrc_params.in". rSOILWAT2 implements additional pedotransfer functions. See documentation entry of "swrc_ptf" for additional details and for guidance on how to implement additional SWRCs and PTFs (issue #315; @dschlaep).

  • Soil density inputs can now represent either matric or bulk density (issue #280; @dschlaep).

    • Automatic conversion between matric and bulk density as needed using the new input type_soilDensityInput.

  • Daily weather inputs that force a simulation are now processed all at once; previously, values were processed for one year at a time during the main simulation loop (issue #311; @dschlaep, @N1ckP3rsl3y).

    • Daily weather inputs are now obtained by readAllWeather() via SW_WTH_read() during SW_CTL_read_inputs_from_disk(), i.e., the same time as other inputs are read from files.
    • Then, weather values are "finalized", i.e., missing values are imputed (e.g., by the weather generator) and scaled with monthly parameters, by finalizeAllWeather() via SW_WTH_finalize_all_weather(); this must occur before the simulation is "initialized" by SW_CTL_init_run().
    • Imputation of missing daily weather values by generateMissingWeather() can be done either by last-observation-carried-forward "LOCF" (which handles all daily weather variables) or by the Markov weather generator (which handles only temperature and precipitation).

  • Daily weather inputs, in addition to the previous variables maximum air temperature, minimum air temperature, and precipitation amount, can now process the following variables (issue #341; @dschlaep, @N1ckP3rsl3y):

    • Cloud cover (can be replaced by shortwave radiation)
    • Wind speed (can be replaced by wind components)
    • Wind speed eastward component (optional)
    • Wind speed northward component (optional)
    • Relative humidity (can be replaced by max/min humidity, specific humidity, dew point temperature, or vapor pressure)
    • Maximum relative humidity (optional)
    • Minimum relative humidity (optional)
    • Specific humidity (optional)
    • Dew point temperature (optional)
    • Actual vapor pressure (optional)
    • Downward surface shortwave radiation (optional)

  • SOILWAT2 gains the ability to calculate long-term climate summaries (issue #317; @N1ckP3rsl3y, @dschlaep).

    • New calcSiteClimate() calculates monthly and annual time series of climate variables from daily weather.
    • New averageClimateAcrossYears() calculates long-term climate summaries.
    • Both functions are based on rSOILWAT2::calc_SiteClimate() which was previously coded in R.
    • This version fixes issues from the previous R version:
      • Mean annual temperature is now the mean across years of means across days within year of mean daily temperature.
      • Years at locations in the southern hemisphere are now adjusted to start on July 1 of the previous calendar year.
      • The cheatgrass-related variables, i.e., Month7th_PPT_mm, MeanTemp_ofDriestQuarter_C, and MinTemp_of2ndMonth_C, are now adjusted for location by hemisphere.

  • SOILWAT2 gains the ability to estimate fractional land cover representing a potential natural vegetation based on climate relationships (using new input veg_method) instead of reading land cover values from input files (issue #318; @N1ckP3rsl3y, @dschlaep).

    • New estimatePotNatVegComposition() estimates fractional land cover representing a potential natural vegetation based on climate relationships. This function is based on rSOILWAT2::estimate_PotNatVeg_composition() which was previously coded in R.
    • New estimateVegetationFromClimate() (which is called by SW_VPD_init_run()) uses veg_method to determine at run time if a simulation utilizes averageClimateAcrossYears() and estimatePotNatVegComposition() to set land cover values instead of using the cover values provided in the input file.
    • This version fixes issues from the previous R version:
      • The C4 grass correction based on Teeri & Stowe 1976 is now applied as documented (rSOILWAT2 issue #218).
      • The sum of all grass components, if fixed, is now incorporated into the total sum of all fixed components (rSOILWAT2 issue #219).

Changes to inputs

  • New inputs via "weathsetup.in" determine whether monthly or daily inputs for cloud cover, relative humidity, and wind speed are utilized; describe which daily weather variables are contained in the weather input files weath.YYYY; and describe units of (optional) input shortwave radiation.
  • New (optional) variables (columns) in weather input files weath.YYYY that are described via "weathsetup.in".
  • New inputs via "siteparam.in" select a soil water release curve swrc_name and determine parameter source has_swrcp, i.e., either estimated via selected pedotransfer function ptf_name or values obtained from new input file "swrc_params.in". Default values "Campbell1974", "Cosby1984AndOthers", and 0 (i.e., use PTF to estimate paramaters) reproduce previous behavior.
  • New input file "swrc_params.in" to provide parameters of the selected soil water release curve (if not estimated via a pedotransfer function) for each soil layer.
  • SOILWAT2 gains type_soilDensityInput as new user input (siteparam.in) with default value 0 (i.e., matric soil density) that reproduces previous behavior.
  • SOILWAT2 gains veg_method as new user input ("veg.in") with default value 0 (i.e., land cover are obtained from input files) that reproduces previous behavior.

SOILWAT2 v6.7.0

  • This version produces exactly the same simulation output as the previous release under default values (i.e., vegetation establishment is turned off).

  • Functionality to calculate and output establishment/recruitment of species now works again and is now covered by tests (issue #336, @dschlaep). Note that this functionality assesses yearly the chances of species to recruit/establish based on simulated daily conditions; however, establishment/recruitment outcomes are not utilized to inform the simulation.

Changes to inputs

  • New input via "<species>.estab" sets the vegetation type of a species establishment parameters'.

SOILWAT2 v6.6.0

  • Random number generators now produce sequences that can be exactly reproduced (@dschlaep).
    • RandSeed() gains arguments "initstate" and "initseq" (and lost "seed") to fully seed a pcg32 random number generator.
    • RandNorm() is now re-entrant and discards one of the two generated values. Compilation with "RANDNORMSTATIC" re-produces the old, not re-entrant implementation.
    • SW_MKV_construct() now only seeds markov_rng (the random number generator of the weather generator) if run as SOILWAT2 using the new input rng_seed; SW_MKV_construct() does not seed markov_rng when run as part of STEPWAT2 or rSOILWAT2 (both of which use their own RNG initialization procedures).
  • SW_WTH_init_run() now also initializes yesterday's weather values (@dschlaep).

Changes to inputs

  • SOILWAT2 gains rng_seed as new user input ("weathsetup.in").