separate the host parameters file from the fates parameter file

[bandre-ucar]

Summary of Issue:

Separate the host parameters file from the fates parameter file.

Requirements or design considerations:

TBD

[rgknox]

@bandre-ucar and I checked in on this. I will work on generating the first dedicated fates netcdf file. After that generating the host-fates api and the pre-processor are orthogonal units of work.

[rgknox]

Here is the current list of FATES parameters that are pulled from the parameter file.

The parameters are associated with four different structures:

    pftcon%    These are CLM PFT parameters that FATES is also using)

    EDParamsShareInst%    These are also pft parameters, and only two of them, and they also seem to be used in fates and CLM)

    EDecophyscon%   These are FATES only PFT variables

    ED_val_      These are not in a structure, they just have this name convention.  They are mostly single parameter values, although one of them is pft indexed.

Variable List: (broken into groups, and after each variable it lists the files it is called from) Variable name in file is in quotes

    EDSharedParamsMod (defined in biogeochem/EDSharedParamsMod.F90)
        EDParamsShareInst%Q10   "q10_mr"
              ./biogeochem/EDPhysiologyMod.F90:
              ./biogeophys/EDPhotosynthesisMod.F90:
        EDParamsShareInst%froz_q10  "froz_q10"
              ./biogeochem/EDPhysiologyMod.F90: 

     EDparamsMod  (defined in main/EDParamsMod.F90:)
          ED_val_grass_spread "grass_spread"
               biogeochem/EDGrowthFunctionsMod.F90:
          ED_val_comp_excln   "comp_excln"
               biogeochem/EDCanopyStructureMod.F90:
         ED_val_stress_mort  "stress_mort"
               biogeochem/EDGrowthFunctionsMod.F90:
          ED_val_dispersal "dispersal"
               (NOT USED)
          ED_val_grperc(maxPft)  "grperc"
               ./biogeochem/EDPhysiologyMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:
          ED_val_maxspread  "maxspread"
               ./biogeochem/EDPatchDynamicsMod.F90:
               ./biogeochem/EDCanopyStructureMod.F90:
               ./main/EDInitMod.F90:
          ED_val_minspread "minspread"
               ./biogeochem/EDCanopyStructureMod.F90:
          ED_val_init_litter "init_litter"
               ./main/EDRestVectorMod.F90:  (THIS SEEMS UNNECESSARY)
               ./main/EDInitMod.F90:
          ED_val_nfires "nfires"
               ./fire/SFMainMod.F90
          ED_val_understorey_death "understorey_death"
               ./biogeochem/EDPatchDynamicsMod.F90:
          ED_val_profile_tol "profile_tol"
               (NOT USED)
          ED_val_ag_biomass "ag_biomass"
               ./fire/SFMainMod.F90:
               ./biogeochem/EDPatchDynamicsMod.F90:
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./biogeochem/EDCanopyStructureMod.F90:
               ./main/FatesHistoryInterfaceMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:

     EDEcophysConType  (./main/EDEcophysConType.F90:)
          EDecophyscon%max_dbh "max_dbh"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%freezetol "freezetol"
               (NOT USED?)
          EDecophyscon%wood_density "wood_density"
               ./biogeochem/EDGrowthFunctionsMod.F90:
          EDecophyscon%alpha_stem "alpha_stem"
               (NOT USED?)
          EDecophyscon%hgt_min "hgt_min"
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDInitMod.F90:
          EDecophyscon%cushion "cushion"
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDInitMod.F90:
          EDecophyscon%leaf_stor_priority "leaf_stor_priority"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%leafwatermax "leafwatermax"
               (NOT USED?)
          EDecophyscon%rootresist "rootresist"
               (NOT USED?)
          EDecophyscon%soilbeta "soilbeta"
               (NOT USED?)
          EDecophyscon%crown "crown"
               ./fire/SFMainMod.F90:
               ./biogeochem/EDCanopyStructureMod.F90:
          EDecophyscon%bark_scaler "bark_scaler"
               ./fire/SFMainMod.F90:
          EDecophyscon%crown_kill "crown_kill"
               ./fire/SFMainMod.F90:
          EDecophyscon%initd "initd"
               ./main/EDInitMod.F90:
          EDecophyscon%sd_mort "sd_mort"
               (NOT USED?)
          EDecophyscon%seed_rain  "seed_rain"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%BB_slope  "BB_slope"
               ./biogeophys/EDPhotosynthesisMod.F90:
          EDecophyscon%root_long  "root_long"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%seed_alloc  "seed_alloc"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%clone_alloc  "clone_alloc"
               ./biogeochem/EDPhysiologyMod.F90:
          EDecophyscon%sapwood_ratio  "sapwood_ratio"
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDInitMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:

      pftcon
          pftcon%woody  "woody"
               ./fire/SFMainMod.F90
               ./biogeochem/EDPatchDynamicsMod.F90:
               ./biogeochem/EDGrowthFunctionsMod.F90
               ./biogeochem/EDCanopyStructureMod.F90:
               ./main/FatesHistoryInterfaceMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:
          pftcon%season_decid  "season_decid"
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDInitMod.F90:
          pftcon%stress_decid  "stress_decid"
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDRestVectorMod.F90:
               ./main/EDInitMod.F90:
          pftcon%evergreen "evergreen"
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDInitMod.F90:
          pftcon%froot_leaf "froot_leaf"
               ./biogeochem/EDCohortDynamicsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:
          pftcon%slatop "slatop"
               ./biogeochem/EDGrowthFunctionsMod.F90:
               ./biogeochem/EDPhysiologyMod.F90:
               ./biogeophys/EDPhotosynthesisMod.F90:
          pftcon%leaf_long "leaf_long"
               ./biogeochem/EDPhysiologyMod.F90:
          pftcon%rootprof_beta "rootprof_beta"
               ./biogeochem/EDPhysiologyMod.F90:
          pftcon%roota_par "roota_par"
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDTypesMod.F90:
          pftcon%rootb_par "rootb_par"
               ./biogeochem/EDPhysiologyMod.F90:
               ./main/EDTypesMod.F90:
          pftcon%lf_flab  "lf_flab"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%lf_fcel  "lf_fcel"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%lf_flig   "lf_flig"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%fr_flab  "fr_flab"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%fr_fcel  "fr_fcel"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%fr_flig  "fr_flig"
               ./biogeochem/EDPhysiologyMod.F90
          pftcon%rhol    "rholvis"  AND "rholnir"
               biogeophys/EDSurfaceAlbedoMod.F90:
          pftcon%rhos  "rhosvis" AND "rhosnir"
               biogeophys/EDSurfaceAlbedoMod.F90:
          pftcon%taul    "taulvis"  AND "taulnir"
               biogeophys/EDSurfaceAlbedoMod.F90:
          pftcon%taus   "tausvis"  AND "tausnir"
               biogeophys/EDSurfaceAlbedoMod.F90:
          pftcon%xl  "xl"
               biogeophys/EDSurfaceAlbedoMod.F90:
          pftcon%c3psn  "c3psn"
               biogeophys/EDPhotosynthesisMod.F90:
          pftcon%flnr  "flnr"
               biogeophys/EDPhotosynthesisMod.F90:
          pftcon%fnitr "fnitr"   CHANGE TO VCMAX25!!!!!
               biogeophys/EDPhotosynthesisMod.F90:
          pftcon%leafcn  "leafcn"
               biogeophys/EDPhotosynthesisMod.F90:
          pftcon%frootcn  "frootcn"
               biogeophys/EDPhotosynthesisMod.F90:
          pftcon%smpsc  "smpsc"
               biogeophys/EDBtranMod.F90:
          pftcon%smpso  "smpso"
               biogeophys/EDBtranMod.F90:

[rgknox]

I uploaded three files involved in creating a stand-alone netcdf file. Aside from the script and the list (explained below), you need the base netcdf parameter file (clm_params_ed.c160808.nc) and nco installed on your computer. Specifically, you need the "ncks" binary that is part of that package.

This file is a bash script that loops through a list of variables that are copied from the default hlm-fates parameter file, into the stand-alone fates parameter file.

This file is the parameter name list that is read from the bash script (second argument).

This is the result netcdf file I generated from the above mentioned script and transfer list.