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CHANGELOG.md

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Unreleased

Changed:

  • Added changes to support groundwater coupling via BMI in #221

1.5.0 - 3 Jan 2024

This version of STEMMUS_SCOPE is only compatible with PyStemmusScope 0.3.0.

Changed:

  • The STEMMUS_SCOPE Matlab Runtime executable now needs version R2023a (#208).

Added:

  • STEMMUS_SCOPE 'BMI'-like mode (#208):
    • The executable can be run in an "interactive" mode. In this mode the model's initialization, time update, and finalization can be called upon separately.
    • The model now will write away BMI-required variables to a state file, which can be used for the Python BMI.
  • A dockerfile for the BMI-enabled STEMMUS_SCOPE model, to make the setup easier.

Fixed:

  • use any() function in solveTridiagonalMatrixEquations.m in #203

1.4.0 - 17 Oct 2023

This version of STEMMUS_SCOPE is only compatible with PyStemmusScope 0.3.0.

Changed:

  • All cond*_ functions are refcatored and moved to +conductivity folder in #189
  • All h_* functions are refcatored and moved to +soilmoisture folder in #193
  • All Air_* functions are refcatored and moved to +dryair folder in 194
  • All Engry_* functions are refcatored and moved to +energy folder in 197
  • Remove ObservationPoints script 200
  • Remove all global variables from STEMMUS_SCOPE script 201

Fixed:

1.3.0 - 22 Jun 2023

This version of STEMMUS_SCOPE is only compatible with PyStemmusScope 0.3.0.

Added:

  • A license file, indicating that the code is under the GNU GPL-3.0 license (#153)
  • A notebook to (more) easily compare the results of different STEMMUS_SCOPE git branches (#177)
  • Changes in the land cover over time are now supported by the model (#182).

Changed:

  • All code has been formatted with MISS_HIT, to improve readability (#147). All new or modified code should follow this style as well.
  • The Constants.m file has been refactored (#158):
    • Removed unused script src/CnvrgnCHK.m
    • Removed unused global variables
    • Replaced Constants.m with io.loadModelSettings and init.defineInitialValues
  • The files calcLambda.m and calcPhi_s.m have been moved to the +equations module (#171)
  • The scripts SOIL1.m and SOIL2.m have been refactored. The code is now in the files UpdateSoilWaterContent.m and updateWettingHistory.m(#180)

Fixed:

  • An error in the sign of NEE has been corrected (#151).

Changes

1.2.0 - 21 Feb 2023

This version of STEMMUS_SCOPE is only compatible with PyStemmusScope 0.2.0.

Changed:

  • The StartInit file has been refactored to improve the code quality, and to remove global variables (#113). This also lead to various bugfixes (#144)
  • Soil initial conditions are now read from a .mat file generated by PyStemmusScope, see the release there.
  • The STEMMUS_SCOPE configuration file has been modified. PLUMBER2 sites are now defined as, e.g. Location=AU-DaS, and the time range for the model is defined as StartTime=2001-01-01T00:00, EndTime=2001-01-02T00:00. See PyStemmusScope for more information.

Changes

1.1.11 - 15 Nov 2022

STEMMUS_SCOPE model that is Octave compatible. The input data and config file can be prepared using PyStemmusScope python package, see readme. Changes are introduced in #128

Changes

1.1.10 - 15 Nov 2022

STEMMUS_SCOPE model.

Added:

  • pull_request_template.md in #116

Removed:

  • src/filesread.m in #107
  • src/set_parameter_filenames.m in #109

Fixed:

  • the function bin_to_csv for storing the values of sim_temp and sim_theta in #103.

Changed:

  • the function filesread is replaced with prepareForcingData in #107
  • a more user-friendly readme in #117

Changes

1.1.9 - 28 Jul 2022

STEMMUS_SCOPE model.

Fixed:

  • function es_fun #81

Changed:

  • era5cli notebook checks sites against land sea mask #79
  • Number of canopy layers in #85
  • Convergence criteria in ebal abs(PSI-PSI1) and stemmus scope max(CHK) in #85
  • Module parallel replaced with for loop in snellius bash script in #91

Removed:

  • Variables for boundary condition settings from Constants.m in #85

Changes

1.1.8 - 08 Jul 2022

STEMMUS_SCOPE model.

Fixed:

  • maximum fractional saturated area in #78

Changed:

  • the parameter of evergreen broadleaf forests in #78

Changes

1.1.7 - 30 Jun 2022

STEMMUS_SCOPE model.

Fixed:

  • Fix vegetation type and T min in #72

Changes

1.1.6 - 29 Jun 2022

STEMMUS_SCOPE model.

Fixed:

  • Fix bugs in DoY and vegetation type processing #67
  • Re-generate the exe file in #70

Changes

1.1.5 - 10 Jun 2022

STEMMUS_SCOPE model updating the scripts StartInit.m and Constants.m to use soil era5 land data in #58

Changed:

  • src/StartInit.m, src/Constants.m and src/filesread.m in #58

Fixed:

  • fix warning message in #57

Added:

  • add InitialConditionPath to config files in #58 and #59
  • add the notebook download_era5_data.ipynb to utils/notebooks in #54

Changes

1.1.4 (1.1.4b) - 11 May 2022

STEMMUS_SCOPE model updating the scripts StartInit.m and Constants.m to modify initial soil moisture in #49

Changed:

  • src/StartInit.m and src/Constants.m in #49
  • use warning off in src/STEMMUS_SCOPE_exe.m in #45

Fixed:

  • Use warning instead of fprintf #45
  • Fix var_t_length so it matches DurationSize in utils/csv_to_nc in #47

Removed:

  • unused scripts in #48

Changes

1.1.3 - 19 Apr 2022

STEMMUS_SCOPE model updating the equation calc_rssrbs.m and refactoring the script soilpropertyread.m to use a high-resolution global soil property datasets in #39

Changed:

  • src/+equations/calc_rssrbs.m, src/Constants.m, src/Initial_root_biomass.m, src/soilpropertyread.m in #39

Fixed:

  • fix the input/output paths in crib config file, see #34
  • replacing the keyboard command with a fprintf statement, see #40

Changes

1.1.2 - 12 Apr 2022

STEMMUS_SCOPE model updating ebal script in #24 and #37.

Added

  • output of NEE in #37
  • documentation in #32 and #33
  • variable DurationSize to config file in #36
  • documentation of how to convert the model output to netcdf files in utils/csv_to_nc/README.md #27
  • python utility for converting the model output to netcdf files in #27

Removed

  • utils/csv_to_nc/write.py and utils/csv_to_nc/read.py in #27

Changed

  • src/ebal.m in #24 and #37
  • src/+io/bin_to_csv.m, src/+io/output_data_binary.m, and
  • src/filesread.m in #24 and #36
  • update utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv in #27
  • replace mean with nanmean in #37
  • readme in #36

Fixed

  • the bash script of the running model on Snellius in #25

Changes

1.1.1 - 02 Feb 2022

STEMMUS_SCOPE model including the simplification of freeze/thaw in subroutines introduced in #14.

Added

  • Python scripts in Utils to convert the output in csv format to netcdf format, see #11
  • The script soilpropertyread.m requires the data of surfdata.nc, see #14.

Removed

  • Files src/+io/create_output_files.m , src/+io/output_data.m, src/SCOPE.exe, in #14.
  • Files src/PHENOLOGY_STATE.m, src/Root_Fraction_General.m, src/VEGETATION_DYNAMIC.m, src/calc_root_growth.m in #14.

Changed

  • src/+equations/Soil_Inertia1.m, src/soilpropertyread.m, src/filesread.m, src/ebal.m, src/StartInit.m , src/STEMMUS_SCOPE.m, src/Initial_root_biomass.m, src/Evap_Cal.m, src/Enrgy_sub.m, src/Constants.m, src/+plot/plots.m, src/+io/select_input.m, src/+io/output_data_binary.m, src/+io/bin_to_csv.m , in #14.

Fixed

  • Output path and forcing path in #10

Changes

1.1.0 - 25 Jan 2022

STEMMUS_SCOPE model including changes from pull requests #4 and #9. The changes are summarized below:

Added

  • Add subfunction and module for "Root Properties"
  • Add modules HT_frez, Initial_root_biomass
  • Add module filesread to get input/output paths and prepare input data
  • Add module soilpropertyread to prepare soil property input data
  • Add module soltir_tp7 to read MODTRAN tp7 file and applies a new MIT algorithm
  • Add functions to convert the outputs format from binary to csv
  • Add the function output_verfication from SCOPE code
  • Add a function to convert timestamp to datetime array from SCOPE code

Changed

  • Modify equation of rssrbs
  • Modify the equation of "soil respiration"
  • Modify modules AirPARM, Air_sub, CnvrgCHK, CondL_Tdisp, CondL_h, CondT_coeff, CondV_DE, CondV_DVg, Cond_k_g, Constants, Density_V, Dtrmn_Z, EfeCapCond, EnrgyPARM, Enrgy_BC, Enrgy_Solve, Enrgy_sub, Evap_Cal, Forcing_PARM, Max_Rootdepth, ObservationPoints, SOIL2, StartInit, TimestepCHK, biochemical, calc_rsoil, calc_sfactor, ebal, hPARM, h_BC, h_sub, hh_Solve
  • Modify STEMMUS_SCOPE
  • Refactor function PlotResults1
  • Remove some of the print statements related to outputs in module IO
  • Refactor function plot in module plot to read csv format instead dat format
  • Update readme

Changes

1.0.0 - 17 Dec 2021

Snapshots of codes used for the paper Integrated modeling of canopy photosynthesis, fluorescence, and the transfer of energy, mass, and momentum in the soil–plant–atmosphere continuum (STEMMUS–SCOPE v1.0.0).

Changes