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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project follows a GNU standard version numbering of major.minor.patch with

  • major for substantial changes to code functionality,

  • minor for additions of modules and functionality, and

  • patch for technical changes and bugfixes without extending the functionality of the code.

  • if applicable, categories to include in the CHANGELOG.md are:

    • Added
    • Changed
    • Deprecated
    • Removed
    • Fixed
    • Security

[Unreleased]

[5.9.7] - 2024-08-30

Contributors

Changed

  • order of freezing of different water soil water components changed: free water freezes last to simply mathematical description of model

[5.9.6] - 2024-08-29

Contributors

Added

  • Utility cdf2grid added to convert grid files in NetCDF format into grid CLM files.
  • Option -json and -raw added to cdf2coord utility to write additional JSON metafile and to write without CLM header.

Changed

  • Check added that dimension must be greater 1 for variable in NetCDF file in cdf2coord.c, input_netcdf.c and coord_netcdf.c.
  • Datatype of longitude/latitude array in coord_netcdf.c changed from float to double for consistency, variable name correctly printed in error messages.
  • Intel and clang compiler recognized in printflags.c.

Fixed

  • Test for null corrected for "output" in fscanoutput.c.
  • Missing break added in switch statement in receiver_coupler.c.
  • Code changed to compile successfully without -DSAFE, -DUSE_NETCDF, and -DUDUNITS compilation flag.
  • Unit for "estab_storage_n" corrected to "gN/m2" in outputvars.cjson.
  • Scaling set to 1 if datatype is not short in cdf2coord.c and cdf2clm.

[5.9.5] - 2024-07-19

Contributors

Fixed

  • Fix a regression for NBP output in fwriteoutput introduced in version 5.9.4

[5.9.4] - 2024-07-18

Contributors

Added

  • Warning added if time step of output is longer than output interval.
  • Cycle length of spinup and number of spinup years checked for positive values in fscanconfig.c.
  • File size of CLM input files is checked for consistency with header and lpjml is stopped accordingly.
  • Utility drainage2cdf added to convert CLM drainage file into a NetCDF file using the soil code NetCDF file (issue #355).

Changed

  • Setting "const_lai_max" renamed to "laimax_const" for consistency.
  • Keyword "laimax_interpolate" renamed to "laimax_manage".
  • Region-specific fractions for residue burning replaced by global parameter "bifratio" and "fuelratio".
  • lpjml now terminates with an error message instead of a warning on invalid country codes to avoid invalid access to country-specific parameters.
  • Country code files can now have only one band. Files with 2 bands are still supported, but region code ignored.
  • Filename and source is written into configuration file created by regridlpj.
  • null allowed for "global_attrs", "inpath", "outpath", "restartpath", "output", and "checkpoint_filename" to disable the feature.

Removed

  • "laimax_interpolate", "firewood", "black_fallow", "till_fallow", "cropsheatfrost", and "grassland_fixed_pft" settings and corresponding code removed (issue #350).
  • Obsolete function daily_setaside.c removed. Function is not necessary any more for coupling to POEM.
  • Obsolete constants removed in conf.h.
  • Unused parameter "residue_rate", "residue_pool", "residue_cn", "residue_fbg" removed.
  • Functions for reading region-specific parameters removed.
  • Obsolete region parameter file manage_reg.cjson removed
  • Obsolete outputs "region", "flux_firewood", "flux_firewood_n" removed.
  • Region definitions removed from managepar.h.

Fixed

  • Typos in error messages corrected in bin2cdf.c and clm2cdf.c.
  • Output of turnover corrected in fprintpar_grass.c.
  • Output of options fixed in openconfig.c if environment variable LPJOPTIONS is set.
  • Calculation of average fixed in statclm.
  • res_remove calculation fixed for residue fires in harvest_crop.c to close carbon and nitrogen balance.
  • Missing update of FLUX_ESTABN_MG added in turnover_tree.c.
  • Function initdrain()corrected to handle river routing files in NetCDF format.

[5.9.3] - 2024-07-18

Contributors

Added

  • Output "nbp" for net biosphere productivity and "tws" for total water storage added.
  • fail added to mail type in lpjsubmit_hpc.
  • Option -map added to cdf2bin and cdf2clm to read map from NetCDF file and write it into JSON metafile.
  • "sim_name" and all other global attributes are written into JSON file for cdf2bin utility.

Fixed

  • Scaling of "littertemp" output fixed.
  • Unit corrected for "rootmoist" output and scaling corrected.
  • Correct number of output files printed in lpjfiles utility if separate output files for each year are enabled.

Changed

  • DEPTH_NAME and BNDS_NAME excluded for search for variable in NetCDF file if no variable name is provided.
  • Check added that dimension must be greater 1 for variable in NetCDF file.

[5.9.2] - 2024-07-18

Contributors

Added

  • fire_grass burns grass leaf biomass based on fire resistence parameter (function did nothing before)
  • Burning of fruits added to fire_tree, although stands with fruit trees currently do not experience fire

Changed

  • Unit and description of FIREF output changed from fire return interval to fire fraction to harmonize output between GlobFirM and SpitFire

Fixed

  • Added missing update of FPCs after fire before establishment

[5.9.1] - 2024-07-11

Contributors

Added

  • Missing regridding of wateruse and livestock density input added in regridlpj.

Changed

  • Compile option -Werror added to stop compilation of icx/gcc after warning. This feature can be disabled by using the -noerror option of configure.sh.
  • Filename and source is written into configuration file created by regridlpj.
  • All missing output indices are printed in case that the "outputvar" array is too short.

Fixed

  • Incorrect scaling removed in utility printharvest.
  • Uninitialized PFT pointer set to first PFT in harvest_stand.c.
  • Uninitialized variable n_attr set to zero in utility printclm.
  • Prescribed land cover is now read correctly if landcover map size differs from number of natural PFTs.
  • Check for land use type WP corrected in landusechange.c (issue #354).
  • Code fixed to remove all warnings if compiled with icx/gcc.
  • regridclm now used for regridding of soil file in regridlpj.
  • Missing seek to offset added in filesexist.c
  • Misplaced deallocation of memory for unit corrected in printclm.

[5.9.0] - 2024-07-08

Contributors

Added

  • Added GPL_HEAT macro to change number of gridpoints per soil layer used for heat convection.
  • Added percolation_heattransfer switch to disable convection/percolation heattransfer.
  • Added littertemp output variable for litter temperature.
  • Added fast implicit crank nicolson heat conduction scheme for non-phase change conditions apply_heatconduction_of_a_day.c.

Changed

  • Replaced soiltemp soil temperature and snow and litter heat conduction routines with update_soil_thermal_state.c; soiltemp remains in the repository for POEM/FMS coupling.
  • Use enthalpy (thermal energy) as state variable for soil thermal regime instead of temperature.
  • Numeric heat conduction method is a finite element enthalpy scheme apply_heatconduction_of_a_day.c.
  • Numeric heat convection method is improved by closing the energy balance for water infil and percolation.
  • Conduction through snow and litter cover is now part of the numerical method for the soil.
  • Snow and litter temperatures are now calculated by interpolating air and top gridpoint temperature.
  • Snow melt by snow temperature greater than 0 deg is removed.
  • Litter heat insulation is now based on literature values for litter thermal conductivity.

[5.8.17] - 2024-06-14

Contributors

Added

  • List of required modules on new PIK cluster added in INSTALL.
  • configure.sh script recognizes new PIK cluster and sets mpiicx/icx compiler accordingly.
  • New site-specific Makefile.hpc2024 and Makefile.icx` for parallel/sequential compilation on new cluster added.
  • New lpjsubmit_hpc slurm script added for new PIK cluster. configure.sh sets symbolic link of lpjsubmit to this script.

Changed

  • All occurrences of the deprecated function MPI_Type_extent replaced by MPI_Type_get_extent to allow compilation with OpenMPI.
  • *.tmp files added to .gitignore.

Fixed

  • Functions mpi_write.c, mpi_write_txt.c, mpi_read_socket.c and mpi_write_socket.c changed to avoid SEGV on new PIK cluster.

[5.8.16] - 2024-06-07

Contributors

Changed

  • .zenodo.org updated to be compliant with PIK publication rules:
    • added "active-development" and "Potsdam Institute for Climate Impact Research" to keywords
    • added Christoph as "contributor", which seems to be the only way to have a visible contact person

[5.8.15] - 2024-05-30

Contributors

Added

  • A preprocessed JSON configuration file can be written if the following setting is added to the *.cjson configuration file:
"json_config_filename" : "output/lpjml_config_restart.json", /* Filename of preprocessed configuration file written or null to disable this feature */

Fixed

  • The right allocated storage for config->coupled_model is checked for NULL in fscanconfig.c.

[5.8.14] - 2024-05-27

Contributors

Fixed

  • fixed PFT pool scaling in mix_veg_grass() and mix_veg_tree()

[5.8.13] - 2024-05-23

Contributors

Changed

  • PFT parameter lai_sapl has been set back to its original value of 0.001 for grasses (tropical, temperate, polar)

[5.8.12] - 2024-05-07

Contributors

Added

  • added link to LPJmL Zenodo archive to README

Changed

  • changed ifndef usage in lpjml_config.cjson to ifdef to avoid confusion

Fixed

  • fixed handling of monthly and daily outputs in iterateyear.c to ensure that last annual timestep of outputs is written after update_annual() is called

[5.8.11] - 2024-04-10

Contributors

Added

  • added four new outputs for managed land: deposition (NDEPO_MG), biological nitrogen fixation (BNF_MG), applied nitrogen (NAPPLIED_MG) and nitrogen establishment flux (FLUX_ESTABN_MG)

[5.8.10] - 2024-04-04

Contributors

Changed

  • In outputvars.cjson, the variable field for output grid has been changed back to "grid" (instead of "soil"). If NetCDF output is written the variable name would be cell id, if raw output is written the variable name would be the coordinates. "grid" is used as generic naming here, long_name is used to describe this exception ("grid information (raw: coordinates, cdf: cell_id)")

[5.8.9] - 2024-03-14

Contributors

Changed

  • NetCDF output files are now in a more ISIMIP3 compliant format, datatype of time, lat, and lon is now double, depth_bnds added to layer specific output. Standard and long name can be specified in outputvars.json.
  • Deprecated function MPI_Extent replaced by MPI_Get_extent in mpi_write.c.
  • Functions create_netcdf.c/create_pft_netcdf.c and create1_netcdf.c/create1_pft_netcdf.c have been merged.
  • Function findcoord() improved to find cell indices, returns now true if coord is within cell.
  • STYLESHEET file converted to markup.
  • Cell size in regridclm is set to cell size of target grid, warning is printed if cell size differs.
  • Format and suffix of output files have been removed in lpjml_config.cjson and are now set by "default_fmt" and "default_suffix":
{ "id" : "npp", "file" : { "name" : "output/mnpp"}},
  • LPJINPATH set to /p/projects/lpjml/input/historical in regridlpj if not defined.
  • "descr" in outputvars.cjson renamed to "long_name".

Added

  • More options added to lpjml_config.cjson to customize format of output:
  "default_fmt" : "raw",     /* default format for output files: "raw","txt","cdf","clm","sock" */
  "default_suffix" : ".bin", /* default file suffix for output files */
  "grid_type" : "short",     /* set datatype of grid file ("short", "float", "double") */
  "flush_output" : false,    /* flush output to file every time step */
  "absyear" : false,         /* absolute years instead of years relative to baseyear (true/false) */
  "rev_lat" : false,         /* reverse order of latitudes in NetCDF output (true/false) */
  "with_days" : true,        /* use days as units for monthly output in NetCDF files */
  "nofill" : false,          /* do not fill NetCDF files at creation (true/false) */
  "baseyear" : 1901,         /* base year for output in NetCDF files */
  • Global attributes for NetCDF output files can be set in the lpjml_config.cjson file:
 "global_attrs" : {"institution" : "Potsdam Institute for Climate Impact Research",
                    "contact" : "", /* name and email address */
                    /* any name and string value can be added: "name" : "value", */
                    "comment" : ""  /* additional comments */
                   }, /* Global attributes for NetCDF output files */
  • "standard_name" for output can be set in outputvars.cjson. If not defined standard name is set to variable name.
  • Chunking defined for NetCDF files if compiled with -DUSE_NETCDF4.
  • Option -metafile added to regridclm and binsum. If metafile contains name of grid file, the filename of the source grid can be omitted:
regridclm -metafile grid_new.clm temp.clm.json temp_new.clm
binsum -metafile mnpp.bin.json anpp.bin
  • NetCDF files can be created with bin2cdf and clm2cdf from the JSON metafiles containing all global attributes:
bin2cdf -metafile soilc_layer.bin.json soilc_layer.nc
clm2cdf -metafile temp.clm.json temp.nc
  • "landcovermap" added to define mapping of the prescribed FPC input to PFTs.
  • -hostfile option added to lpjrun.
  • New utilities added:
    • cmpbin - compares binary ouput files
    • statclm - prints minimum, maximum and average of clm files
    • regriddrain - regrids drainage file to new grid
  • Option -metafile and -f added to mathclm.
  • cdf2clm stores all global attributes of NetCDF file in JSON metafile if -json option is set.
  • Option -nopp added to lpjml. This option disables preprocessing of the config file by cpp.
  • Option -ofiles added to lpjml and lpjcheck to print list of all available output files.
  • Option -pedantic added to lpjcheck and lpjml to stop on warning.
  • Option -json added to regridclm and regridsoil utilities to create additional JSON metafiles.
  • Compile flag -DSTRICT_JSON added to enable more strict syntax checking of JSON files.
  • Remark message in fscankeywords.c added if number instead of string is used in JSON file.

Fixed

  • Missing deallocation added in freeconfig.c and memory leak in fscanpftpar.c fixed.
  • Missing argument after option handling fixed in cdf2bin and countr2cdf.
  • Missing $dir/ added to manure data in regridlpj.
  • Correct default landuse, sowing data and crop PHU file set in regridlpj.

[5.8.8] - 2024-03-07

Contributors

Fixed

  • missing family names added in CITATION.cff

Changed

  • renamed double_harvest.c to separate_harvests.c and update_double_harvest.c to update_separate_harvests.c and changed entries in Makefiles accordingly
  • renamed functions double_harvest() to separate_harvests() and update_double_harvest() to update_separate_harvests() throughout the code
  • renamed the struct Double_harvest to Separate_harvest and the variable of type Separate_harvest in struct Pftcrop from dh to sh
  • renamed double_harvest flag in struct Config to separate_harvests

[5.8.7] - 2024-03-06

Contributors

Added

  • new output PFT_WATER_SUPPLY to calculate water stress PFT-specific.

Changed

  • output writing for the new output (conf.h , outputvar.cjson , createpftnames.c , fwriteoutput.c , outputsize.c , water_stressed.c).
  • isopen() call removed (fwriteoutput.c).

[5.8.6] - 2024-02-29

Fixed

  • Divsion by zero avoided for calculation of nc_ratio in ndemand_tree.c and ndemand_grass.c (issue #341).
  • Default directory for input files to current directory set and directory created in regridlpj.
  • Correct id 11 set for "tamp" input in input.cjson (issue #347).
  • Correct filename used in error message in utility mathclm.
  • Datatype of Version 4 CLM files correctly handled in cutclm, catclm, mergeclm, regridclm.

Changed

  • Hard coded CFT indices (e.g. MAIZE) have been replaced by their names.
  • Datatype of bmgr_harvest_day_nh and bmgr_harvest_day_nh changed to int.
  • Function freadseed() used in freadrestartheader.c.
  • First value of CO2 data file used for simulation years before first year of CO2 data.
  • CO2 data replaced by TRENDY data in input.cjson.

Added

  • Man page for regridclm and regridsoil added.
  • New keywords "cft_fertday_temp" and "cft_fertday_tropic" added in lpjparam.cjsonto specify the CFT names where the fertilizer application dates are taken from for grasslands.
  • Missing filename of tillage input added to lpjfiles utility.
  • Option -h added to lpjsubmit. Options -v and -l added to configure.sh.
  • New keyword "error_limits" defined in lpjparam.cjson to set maximum balance errors allowed in simulation:
 "error_limits" :
    {
      "carbon" : 1.0,       /* maximum error in local carbon balance (gC/m2) */
      "nitrogen" : 0.2,     /* maximum error in local nitrogen balance (gN/m2) */
      "water_local" : 1.5,  /* maximum error in local water balance (mm) */
      "water_global" : 1e-3 /* maximum error in global water balance (mm) */
    },

Removed

  • Option --propagate removed from srun in lpjsubmit_slurm.
  • Hard-coded parameter k_l removed in littersom.c.
  • Parameter "residues_in_soil_notillage" removed.
  • Parameter "co2_p" removed.
  • Keyword in "till_startyear" removed from lpjml_config.cjson.

[5.8.5] - 2024-01-31

Contributors

Added

  • added .zenodo.json for interaction with zenodo archives
  • added CITATION.cff file

Changed

  • updated AUTHORS file

[5.8.4] - 2024-01-22

Contributors

Fixed:

  • Removed lines 240 and 241 in landuse/annual_biomass_tree.c to get rid of the carbon balance error, which shows up in cells with significant bioenergy tree fractions in the landuse input.

[5.8.3] - 2024-01-21

Contributors

Added

  • allowed range for coordinates checked in readcoord().
  • allowed formats ("raw", "clm", "clm2") for input files checked in openmetafile().
  • Output scaling added to writearea.c.

Changed

  • Error messages changed for more clarity.

Fixed

  • NetCDF output for grid file corrected if cells are skipped.
  • var_len correctly set for input with no time axis in openclimate_netcdf.c.

[5.8.2] - 2023-12-21

Contributors

Changed

  • wateruse from "yes" to "all"
  • sowing_date_option from "fixed_sdate" to "prescribed_sdate"
  • crop_phu_option from "new" to "prescribed"
  • tillage_type from "all" to "read"
  • residue_treatment from "fixed_residue_remove" to "read_residue_data"
  • grazing from "default" to "livestock"
  • prescribe_lsuha from FALSE to TRUE
  • set nspinup to 420 instead of 390 for LU spinup
  • updated paths to land management input files in input.cjson
  • set all available LandInG1.0 inputs as the default option

[5.8.1] - 2023-12-11

Contributors

Added

  • tmin, tmax, humid GSWP3-W5E5 inputs added to input.cjson.
  • missing parameters added in lpjparam_non.cjson and pft_non.cjson.

Changed

  • set gml.noaa data as default CO2 input.
  • GSWP3-W5E5 climate is now the default.
  • regridlpj utility script updated for new inputs

Removed

  • GLDAS climate input removed.

Fixed

  • scaling fixed for daily output and unit 1/second in fwriteoutput.c (issue #332).
  • #ifdef and #elif statements fixed in lpjml_config.cjson and input.cjson.
  • computation of root biomass based on carbon fixed in nuptake_grass and nuptake_tree (issue #330)
  • fixed bug in allocation_tree (issue #330)

[5.8.0] - 2023-11-30

Contributors

Added

  • new keyword "cultivation_types" added to specify an array of cultivation types read from the pft.cjson file:
  "cultivation_types" : ["none","biomass","annual crop"],
  • wood plantation and agricultural tree PFTs added to pft.cjson.
  • '"k_est"' establishment density array added for agricultural trees to "countrypar" in manage_irrig_systems_with_dummy_laimax_data.cjson.
  • Makros to select different climate (CRU_MONTHLY, CRU_NETCDF, GLDAS) as well as land use, fertilizer and manure (OLD_LU, MADRAT) inputs added to input.cjson.
  • Makro to disable nitrogen cycle (WITHOUT_NITROGEN) added to lpjml_config.cjson.
  • Makros definition and description added to lpjml_config.cjson.

Changed

  • file ending from js to cjson.
  • renamed lpjml.cjson to lpjml_config.cjson.
  • extended input.cjson to include CRU, GSWP3-W5E5 and GLDAS climate inputs and LandInG, MADRAT and "Old" land use, fertilizer and manure inputs.
  • Moved mappings from input.cjson to lpjml_config.cjson.
  • Moved soil depths array and fuel bulk density factors from soil.cjson to lpjparam.cjson.

Removed

  • lpjml_*js, param_*js, lpjparam_*js, pft_*.js, input_*.js and manage_*.js files for specific projects.

[5.7.10] - 2023-11-13

Contributors

Added

  • name of grid file and "terr_area" output file written to output JSON files. A link to the corresponding JSON file is added.
  • list of utilities added to INSTALL file.
  • -json flag added to cdf2clm utility.
  • last year of CO2 data is checked at run time and last year of simulation is changed accordingly.

Changed

  • fscanfloat() accepts now also integer input.

Removed

  • obsolete constant definitions in conf.h.

Fixed

  • opening of grid file in JSON metafile format fixed in opencoord().
  • default soil map is set for soil data in NetCDF format.
  • missing carbon influx added to NBP calculation in flux_sum.c.

[5.7.9] - 2023-10-23

Contributors

Changed

  • constant wood density has been replaced by PFT-specific parameter "wood_density".

Removed

  • Unused flag "biomass_grass_harvest" removed from configuration.

Fixed

  • update of pft->establish.nitrogen corrected in turnover_tree.c.
  • C and N in manure from grazing livestock goes to litter (as described in Heinke et al. 2023 instead of going to soil pools directly.

[5.7.8] - 2023-09-22

Contributors

Fixed

  • bug in landusechange.c where land transfers between rainfed and irrigated setaside stands were not taken into account when determining rainfed and irrigated areas to deforest/regrow
  • false positive carbon balance errors in turnover_tree.c if the code is compiled with CHECK_BALANCE switch

[5.7.7] - 2023-09-20

Contributors

Added

  • grassland specific variables deficit_lsu_ne and deficit_lsu_mp added to fprint_grassland.c and therefore are printed by lpjprint.

Removed

  • obsolete definition of constants removed in conf.h.

Fixed

  • division by zero resulting in a floating point exception if lpjml is run with -fpe option fixed in littersom.c and harvest_stand.c.
  • index in "cft_nir" output is now correctly calculated for agriculture_tree/agrculture_grass stands in distribute_water.c.
  • pft->npp_bnf set to zero for the auto fertilization setting in the N uptake functions. Fertilization only applied if N deficit is greater than zero.

[5.7.6] - 2023-09-11

Added

  • reallocation of N added in allometry_tree.c if tree height exceeds the maximum height.
  • reproduction costs for nitrogen added to turnover_tree.c.
  • missing output "harvestc_agr" updated and written to file.

Changed

  • check for sum>1 for warnings has been replaced by sum>1+epsilon in getlanduse().
  • ml.landfrac scaling of output has been replaced by acual stand fraction.
  • output_gbw_* functions have been merged into one output_gbw function.

Removed

  • misplaced CFT_AIRRIG update has been removed from daily_woodplantation.c.

Fixed

  • missing #include "grass.h" added in sowingcft.c.
  • arguments of setaside calls in annual_woodplantation.c and annual_biomass_tree.c have been corrected.
  • update of LITFALLN corrected in timber_burn.c.
  • output written to correct N2O_DENIT_* file in denitrification.c.
  • missing reservoirfrac added to scaling for outputs in daily_agriculture_grass.c and daily_agriculture_tree.c.

[5.7.5] - 2023-08-23

Added

  • outputs:
    • IRRIG_STOR
    • RIVERVOL
    • SWC_VOL

Changed:

  • unit of output RES_STORAGE changed from hm3 to dm3 to be in line with IRRIG_STOR, RIVERVOL, LAKEVOL, SWC_VOL

Fixed

  • check for land-use fractions to not exceed 100% after scaling with landfrac, re-scale to 100%, print warning see !173
  • add turnover before allocation in cultcftstand to prevent sporadic C balance errors when running with intercrops, see!175
  • number of wet days not read if daily precipitation input is used. A warning is additionally printed to set "random_prec" to false.
  • boolean "river_routing" is read before "with_lakes" flag to avoid uninitialized variable.

[5.7.4] - 2023-08-17

Changed

  • changed quadratic soil evaporation function to sigmoid form and a minimum amount of evaporation of 5% of the available energy, following Sun et al. 2013, as described in !168

[5.7.3] - 2023-08-16

Fixed

  • correct accounting of blue water transpiration on agriculture stands in outputs
  • missing variable initialization for bioenergy grass
  • landuse change from irrigated to rainfed setaside moved area to wrong target setaside

[5.7.2] - 2023-08-11

Changed:

  • removed timestep attributes (monthly/annual) in all output descriptions that are not timestep specific

Added

  • outputs:
    • PFT_WATER_DEMAND: PFT specific water demand
    • RD: dark respiration
    • NDEPOS: total N deposition as sum of NH4 and NO3 deposition

[5.7.1] - 2023-08-10

Fixed

  • wrong use of &f instead of f, in fscanparam.c. Bug was introduced in version 5.6.26 and caused that parameter files could not be read properly

[5.7.0] - 2023-08-10

Added

  • land fraction can now be read from file, with a new flag "landfrac_from_file" and a new input "landfrac"
  • If setting "landfrac_from_file : true" cell areas in LPJmL are scaled down by land fraction from input file. If land fraction is zero, land fraction is set to minlandfrac and a warning is printed.
  • new flag "with_lakes" defined
  • new outputs "terr_area", "land_area" and "lake_area" defined writing the terrestrial area (land and lakes), land area and lake area of each cell
  • new parameters "minlandfrac" and "tinyfrac" added to lpjparams.js
  • option -area filename added to the printglobal utility to scale with the cell areas read from the file specified.

Changed

  • Lake fraction and land-use fractions are rescaled by the reciprocal of land fraction. If lake fraction is greater than one, lake fraction is set to one and a warning is printed.
  • Lakes can be enabled without river routing by setting "with_lakes" : true. Variable dmass_lake is always written to restart file.
  • lake fraction is read in utility lpjprint and printed
  • flag "shuffle_spinup_climate" only read if "nspinup" is non-zero.
  • Terrestrial area and harvest fraction are read in utility printharvest. Output format changed to CSV.

[5.6.27] - 2023-08-08

Removed

  • removed large chunks of code in allocation_daily_crop.c that was inactive

Fixed

  • fixed output PFT_VEGC to not include bm_inc.nitrogen for crops in daily_agriculture.c
  • fixed global flux summation for flux.soil.carbon and flux.soil.nitrogen (+= instead of =), bug was introduced in version 5.6.25

[5.6.26] - 2023-08-07

changed

  • avoid daily leaf turnover for biomass grass and harvest leaf turnover as dead biomass at harvest event instead (reduces litter and increases harvest)
  • introduce harvest dates depending on green/brown harvest instead of C threshold for biomass grass
  • literature-based C/N ratios and fn_turnover for biomass grass depending on green/brown harvest configuration
  • results and literature references can be found in issue #275.

Added

  • introduced #define flag to change from green harvest (default) to brown harvest: #define BMGR_BROWN
  • two options include green harvest (fresh biomass, high N content - usually used for biofuels) and brown harvest (dry biomass, high lignin content, low N content - usually used for combustion)
  • brown harvest uses later harvest dates (defined in lpjparam.js) and higher N recovery (as lower fn_turnover defined in pft.js) than green harvest
  • the #define flag is required to read the correct flag-specific parameter from the lpjparam.js and pft.js, see issue #311

[5.6.25] - 2023-07-29

Added

  • New outputs added for N fluxes from timber extraction and for N pools in wood product pools
  • New outputs added for estab_storage C and N
  • Added missing N fluxes, estab_storage, and reservoirs to globalflux output
  • Added new fluxes to man pages

Fixed

  • Corrected/added units in comments in output.h
  • Corrected units in flux_sum man page
  • Corrected N2O_DENIT output, which now no longer also includes N2O_NIT values
  • Corrected writing of mineral N pools to outputs, so that also mineral N in frozen soil layers is included
  • Corrected writing of VEGN for crops, so that bm_inc.nitrogen is no longer included to avoid double accounting

Removed

  • Removed unecessary initialization of output variables to zero in update_annual.c, which is done in initoutputdata.c

[5.6.24] - 2023-07-29

Fixed

  • The number of bands is now correctly checked for the read_residue_data input.

[5.6.23] - 2023-07-28

Changed

  • Instead of the soil code the index of the grid cell is written into the NetCDF file for "grid" output.

[5.6.22] - 2023-07-27

Changed

  • Configuration files lpjml_netcdf.js, lpjml_non.js, param_non.js, and lpjparam_non.js updated to latest lpjml version.

Removed

  • Predefined daily outputs ("d_lai"-"d_pet") and corresponding functions removed.

  • Version numbers removed from man pages.

Fixed

  • Variable issocket always initialized to FALSE in readfilename.c.

[5.6.21] - 2023-07-21

Changed

  • Flag "nitrogen_coupled" disabled for lpjml offline runs. Water stress is always coupled with nitrogen stress. Only if lpjml is compiled with -DCOUPLING_WITH_FMS flag is enabled.

  • Flag "new_trf" renamed to "transp_suction_fcn".

[5.6.20] - 2023-07-13

Added

  • New flags "fix_co2" and "fix_co2_year" added.

Changed

  • Flag "istimber" renamed to "luc_timber".

  • Flag "new_phenology" renamed to "gsi_phenology".

  • Flag "shuffle_climate" renamed to "shuffle_spinup_climate".

  • The settings for fixed input data have been updated. For climate and N deposition input an interval can be specified from which data is taken after the specified year. In can specified whether random shuffling or cycling is used:

"fix_climate" : false,                /* fix climate after specified year */
"fix_climate_year" : 1901,            /* year after climate is fixed */
"fix_climate_interval" : [1901,1930],
"fix_climate_shuffle" : true,          /* randomly shuffle climate in the interval */
"fix_deposition_with_climate" : false, /* fix N deposition same as climate */
"fix_deposition" : false,              /* fix N deposition after specified year */
"fix_deposition_year" : 1901,          /* year after deposition is fixed */
"fix_deposition_interval" : [1901,1930],
"fix_deposition_shuffle" : true,       /* randomly shuffle depositions in the interval */
"fix_landuse" : false,                 /* fix land use after specfied year */
"fix_landuse_year" : 1901,             /* year after land use is fixed */
"fix_co2" : false,                     /* fix atmospheric CO2  after specfied year */
"fix_co2_year" : 1901,                 /* year after CO2 is fixed */

Removed

  • Obsolete flag "const_climate" removed.

[5.6.19] - 2023-07-06

Added

  • Help option -h added to bin2cdf and clm2cdf utility.

  • Target lpjcheck added to Makefile to create only the lpjcheck utility.

Changed

  • The version of all man pages has been set to the LPJmL version number, date of last modification removed.

  • The different versions of the utilities have been replaced by a reference to the LPJmL version.

Removed

  • All html files have been removed from the repository.

  • Obsolete link lpj to lpjml removed.

[5.6.18] - 2023-07-04

Fixed

  • Soil array wpwp is now correctly initialized with soilpar->wpwp for the "prescribed_soilpar" setting.

[5.6.17] - 2023-06-30

Fixed

  • Replaced logical or by logical and in survive.c. This solves issue #309.

[5.6.16] - 2023-06-30

Fixed

  • Removed excess pft->nind in all harvest routines in harvest_stand.c.

[5.6.15] - 2023-06-30

Added

  • Check for matching size of discharge queues read from restart file added to initriver() function in initdrain.c. If the size differs from the value calculated from the river lengths the queues will be resized and initialized to zero. Error message is additionally printed.

[5.6.14] - 2023-06-08

Removed

  • Support for the deprecated *.conf configuration file format has been removed. Only JSON files are allowed for configuration files and metafiles for input.

  • Man pages for the description of the *.conf file format removed.

Changed

  • Strings in JSON configuration files can now be longer than 256 characters.

[5.6.13] - 2023-05-16

Added

  • Missing update of "harvestc" and "harvestn" output added in annual_biomass_tree.c, annual_woodplantation.c, daily_agriculture_tree.c, and annual_agriculture_tree.c.

[5.6.12] - 2023-05-12

Added

  • Missing agsub litter pool added to "litc", "litn", "mg_litc", "litc_agr", "mgrass_litc", "mgrass_litn" outputs and in global flux of litc.

  • Output of "litc_ag" and "litc_all" now written to output file.

Changed

  • Item ag in struct Litter renamed to agtop.

  • Functions litter_ag_grass(), litter_ag_nitrogen_tree(), litter_ag_sum(), litter_ag_sum_quick(), litter_ag_tree() renamed to litter_agtop_grass(), litter_agtop_nitrogen_tree(), litter_agtop_sum(), litter_agtop_sum_quick(), litter_agtop_tree().

  • Index in outnames array in fwriteoutput.c corrected for "mgrass_soilc", "mgrass_soiln", "mgrass_litc", "mgrass_litn"outputs.

[5.6.11] - 2023-05-11

Fixed

  • Invalid access to pointers soil->wsat-soil->wpwp has been replaced by access to layer specific data soil->wsat[l]-soil->wpwp[l] in infil_perc_rain.c and infil_perc_irr.c. See issue #303.

[5.6.10] - 2023-05-10

Added

  • PFT specific output for biological nitrogen fixation with grid and PFT scaling in npp_contr_biol_n_fixation.c and biologicalNfixation.c.

Changed

  • Adjusted optimum temperature limits ("temp_bnf_opt") of herbaceous PFTs for NPP controled biological nitrogen fixation in pft.js.

[5.6.9] - 2023-05-10

Added

  • Missing break statement added in harvest_stand.c. See issue #302

  • Missing deallocation of decomp_litter_pft added in freesoil.c.

  • Missing deallocation of with_tillage_filename added in freeconfig.c.

Changed

  • If input comes from socket connection the existence of the file is not checked anymore.

  • The memcpy arguments in cpl.h are now in the right order.

[5.6.8] - 2023-04-28

Added

  • flag "start_coupling" added in configuration file. If lpjml is coupled to an external model via
  "coupled_model" : "model",

this flag allows so set a year when input is received from the external model. Before that year input is read from input file. If flag is omitted or set to null coupling starts at the first year.

Changed

  • For input received from an external model a file name can additionally be specified where input is read from before the specified coupling year:
  "with_tillage" : { "fmt" : "clm", "socket" : true, "name" : "tillage.clm"},

  • lpjcheck and lpjml checks for specified filenames if they are necessary for the coupled run

  • JSON metafiles are also created for NetCDF output

[5.6.7] - 2023-04-27

Added

  • CHANGELOG.md added see issue #298

Changed

  • leading zeros removed in patch identifier of the version number

History

  • all versions prior to 5.6.7 have not been documented by a changelog or similar but in the respective merge requests (internal link accessible at PIK only)