Contents

• Introduction
• Code Structure
  • Source Code Organization
  • Calling Tree
  • Operating Modes
  • Initialization
  
  
• Data Structures
  • Hierarchy of Grid Scales
    • Adding Quantities to the CLM Data Structures
  • Decomposition and Clumps
  • Filters
  • Loop Composition
  • Averaging from a Subgrid Level to an Encompassing Subgrid Level
  
  
• Input and Output Files
  • Surface Data Input
  • History Dataset Fields
    • History Output on the Model Grid
    • History Output on the RTM Grid
  • Restart Datasets
  • Initial Datasets
  
  
• Error Conditions
  • Energy and water balance errors
  
  
• Bibliography
• ProTEX Source Code Documentation
  • Module BalanceCheckMod (File: BalanceCheckMod.F90)
    • BalanceCheck
  • Module BareGroundFluxesMod (File: BareGroundFluxesMod.F90)
    • BareGroundFluxes
  • Module Biogeophysics1Mod (File: Biogeophysics1Mod.F90)
    • Biogeophysics1
  • Module Biogeophysics2Mod (File: Biogeophysics2Mod.F90)
    • Biogeophysics2
  • Module BiogeophysicsLakeMod (File: BiogeophysicsLakeMod.F90)
    • BiogeophysicsLake
  • Module CanopyFluxesMod (File: CanopyFluxesMod.F90)
    • CanopyFluxes
    • Stomata
  • Module DGVMAllocationMod (File: DGVMAllocationMod.F90)
    • Allocation
  • Module DGVMEcosystemDynMod (File: DGVMEcosystemDynMod.F90)
    • EcosystemDynini
    • DGVMEcosystemDyn
    • DGVMRespiration
    • Phenology
    • FireSeason
    • LitterSOM
  • Module DGVMEstablishmentMod (File: DGVMEstablishmentMod.F90)
    • Establishment
  • Module FireMod (File: DGVMFireMod.F90)
    • Fire
  • Module KillMod (File: DGVMKillMod.F90)
    • Kill
  • Module LightMod (File: DGVMLightMod.F90)
    • Light
  • Module DGVMMod (File: DGVMMod.F90)
    • lpj
    • lpjreset1
    • lpjreset2
    • histDGVM
    • resetTimeConstDGVM
    • resetWeightsDGVM
    • gatherWeightsDGVM
    • set_dgvm_filename
    • BuildNatVegFilter
  • Module MortalityMod (File: DGVMMortalityMod.F90)
    • Mortality
  • Module ReproductionMod (File: DGVMReproductionMod.F90)
    • Reproduction
  • Module restDGVMMod (File: DGVMRestMod.F90)
    • restart_dgvm
  • Module TurnoverMod (File: DGVMTurnoverMod.F90)
    • Turnover
  • Module DUSTMod (File: DUSTMod.F90)
    • DustEmission
    • DustDryDep
    • Dustini
  • Module DriverInitMod (File: DriverInitMod.F90)
    • DriverInit
  • Module FracWetMod (File: FracWetMod.F90)
    • FracWet
  • Module FrictionVelocityMod (File: FrictionVelocityMod.F90)
    • FrictionVelocity
    • StabilityFunc
    • StabilityFunc2
    • MoninObukIni
  • Module Hydrology1Mod (File: Hydrology1Mod.F90)
    • Hydrology1
  • Module Hydrology2Mod (File: Hydrology2Mod.F90)
    • Hydrology2
  • Module HydrologyLakeMod (File: HydrologyLakeMod.F90)
    • HydrologyLake
  • Module QSatMod (File: QSatMod.F90)
    • QSat
  • Module RtmMod (File: RtmMod.F90)
    • Rtmgridini
    • Rtmlandini
    • Rtmfluxini()
    • Rtmriverflux
    • UpdateInput
    • Rtm
    • UpdateGlobal
    • restart_rtm
  • Module RunoffMod (File: RunoffMod.F90)
    • set_roflnd
    • set_rofocn
    • set_proc_rof_bounds
    • UpdateRunoff
    • get_proc_rof_total
    • get_proc_rof_bounds
    • get_proc_rof_global
  • Module STATICEcosysDynMod (File: STATICEcosysDynMod.F90)
    • EcosystemDynIni
    • EcosystemDyn
    • interpMonthlyVeg
    • readMonthlyVegetation
  • Module SnowHydrologyMod (File: SnowHydrologyMod.F90)
    • SnowWater
    • SnowCompaction
    • CombineSnowLayers
    • DivideSnowLayers
    • Combo
    • BuildSnowFilter
  • Module SoilHydrologyMod (File: SoilHydrologyMod.F90)
    • SurfaceRunoff
    • Infiltration
    • SoilWater
    • Drainage
  • Module SoilTemperatureMod (File: SoilTemperatureMod.F90)
    • SoilTemperature
    • SoilThermProp
    • PhaseChange
  • Module SurfaceAlbedoMod (File: SurfaceAlbedoMod.F90)
    • SurfaceAlbedo
    • SnowAlbedo
    • SoilAlbedo
    • TwoStream
    • SnowAge
  • Module SurfaceRadiationMod (File: SurfaceRadiationMod.F90)
    • SurfaceRadiation
  • Module TridiagonalMod (File: TridiagonalMod.F90)
    • Tridiagonal
  • Module VOCEmissionMod (File: VOCEmissionMod.F90)
    • VOCEmission
  • Module abortutils (File: abortutils.F90)
    • endrun
  • Module accFldsMod (File: accFldsMod.F90)
    • initAccFlds()
    • updateAccFlds
    • initAccClmtype
  • Module accumulMod (File: accumulMod.F90)
    • init_accum_field
    • print_accum_fields
    • extract_accum_field_sl
    • extract_accum_field_ml
    • update_accum_field_sl
    • update_accum_field_ml
    • restart_accum
  • Module areaMod (File: areaMod.F90)
    • areaini
    • areaave
    • areamap
    • areaovr
    • cellarea_regional
    • cellarea_global
    • celledge_regional
    • celledge_global
    • areaini_point
    • areamap_point
    • areaovr_point
    • mkmxovr
  • Module atm_lndMod (File: atm_lndMod.F90)
    • atmlnd_ini
    • atmlnd_drv
  • Module atmdrvMod (File: atmdrvMod.F90)
    • atmdrv
    • atm_getgrid
    • atm_openfile
    • atm_readdata
    • interpa2si
    • interpa2s
  • Module clm_csmMod (File: clm_csmMod.F90)
    • csm_setup
    • csm_shutdown
    • csm_initialize
    • csm_recvgrid
    • csm_sendalb
    • csm_dosndrcv
    • csm_recv
    • csm_send
    • csm_flxave
    • compat_check
    • csm_compat
    • restart_coupler
    • global_sum_fld2d
    • global_sum_fld1d
  • Module clm_varcon (File: clm_varcon.F90)
  • Module clm_varctl (File: clm_varctl.F90)
  • Module clm_varpar (File: clm_varpar.F90)
  • Module clm_varsur (File: clm_varsur.F90)
    • varsur_alloc
    • varsur_dealloc
  • Module clmtype (File: clmtype.F90)
  • Module clmtypeInitMod (File: clmtypeInitMod.F90)
    • initClmtype
    • init_pft_type
    • init_column_type
    • init_landunit_type
    • init_gridcell_type
    • init_energy_balance_type
    • init_water_balance_type
    • init_pft_pstate_type
    • init_pft_ecophys_constants
    • init_pft_DGVMecophys_constants
    • init_pft_energy_type
    • init_pft_wstate_type
    • init_pft_pdgvstate_type
    • init_pft_eflux_type
    • init_pft_mflux_type
    • init_pft_wflux_type
    • init_pft_cflux_type
    • init_pft_vflux_type
    • init_pft_dflux_type
    • init_column_pstate_type
    • init_column_estate_type
    • init_column_wstate_type
    • init_column_cstate_type
    • init_column_eflux_type
    • init_column_wflux_type
    • init_landunit_pstate_type
    • init_gridcell_dgvstate_type
    • init_gridcell_pstate_type
    • init_atm2lnd_state_type
    • init_lnd2atm_state_type
    • init_atm2lnd_flux_type
    • init_lnd2atm_flux_type
    • init_gridcell_wflux_type
  • Module controlMod (File: controlMod.F90)
    • control_init
    • control_spmd
    • control_print
  • Module decompMod (File: decompMod.F90)
    • initDecomp
    • get_nclumps
    • get_clump_cell_id_coord
    • get_clump_owner_id
    • get_clump_ncells_proc
    • get_clump_ncells_id
    • get_clump_coord_id
    • get_gcell_info
    • get_clump_gcell_info
    • get_clump_bounds
    • get_proc_bounds
    • get_proc_total
    • get_proc_global
    • get_proc_clumps
    • get_gcell_xyind
    • map_dc2sn_sl_real
    • map_dc2sn_sl_int
    • map_dc2sn_ml1_real
    • map_dc2sn_ml1_int
    • map_sn2dc_sl_real
    • map_sn2dc_sl_int
    • map_sn2dc_ml1_real
    • map_sn2dc_ml1_int
    • get_sn_land1d
    • get_sn_cols1d
    • get_sn_pfts1d
  • do_close_dispose (File: do_close_dispose.F90)
  • do_restwrite (File: do_restwrite.F90)
  • driver (File: driver.F90)
    • write_diagnostic
  • Module fileutils (File: fileutils.F90)
    • get_filename
    • set_filename
    • getfil
    • putfil
    • opnfil
    • getavu
    • relavu
    • shell_cmd
  • Module filterMod (File: filterMod.F90)
    • initFilters
  • getdatetime (File: getdatetime.F90)
  • Module histFileMod (File: histFileMod.F90)
    • masterlist_printflds
    • masterlist_addfld
    • htapes_build
    • masterlist_make_active
    • masterlist_change_timeavg
    • htapes_fieldlist
    • htape_addfld
    • update_hbuf
    • update_hbuf_field
    • hfields_normalize
    • hfields_zero
    • htape_create
    • htape_timeconst
    • hfields_write
    • hfields_1dinfo
    • htapes_wrapup
    • restart_history
    • getname
    • getflag
    • list_index
    • set_hist_filename
    • add_fld1d
    • add_fld2d
    • pointer_index
    • add_subscript
  • Module histFldsMod (File: histFldsMod.F90)
    • initHistFlds
  • iniTimeConst (File: iniTimeConst.F90)
  • iniTimeVar (File: iniTimeVar.F90)
    • mkarbinit
  • Module inicFileMod (File: inicFileMod.F90)
    • inicfile
    • inicfields
    • inicperp
    • do_inicwrite
    • set_init_filename
  • Module initGridcellsMod (File: initGridCellsMod.F90)
    • initGridcells
    • landunit_veg_compete
    • landunit_veg_noncompete
    • landunit_special
    • landunit_crop_noncompete
    • initGridcellsGlob
  • Module initializeMod (File: initializeMod.F90)
    • initialize
    • header
  • Module iobinary (File: iobinary.F90)
    • readin_1d_array_int
    • readin_1darray_real
    • readin_2d_arrayint
    • readin_2darray_real
    • wrtout_1d_array_int
    • wrtout_1d_array_real
    • wrtout_2d_array_int
    • wrtout_2darray_real
    • getnum
  • Module lnd2atmMod (File: lnd2atmMod.F90)
    • lnd2atm
    • makel2a
  • Module lp_coupling (File: lp_coupling.F90)
    • lp_coupling_init
    • lp_coupling_finalize
    • alltoall_clump_to_chunk_init
    • alltoall_clump_to_chunk
    • alltoall_chunk_to_clump
    • mkglacier
  • Module mkgridMod (File: mkgridMod.F90)
    • mkgrid_offline
    • read_grid_offline
    • create_grid_offline
    • mkgrid_cam
  • Module mklai (File: mklai.F90)
    • mklai
  • mklanwat (File: mklanwat.F90)
  • Module mkpft (File: mkpft.F90)
    • mkpfts
  • mkrank (File: mkrank.F90)
  • mksoicol (File: mksoicol.F90)
  • mksoitex (File: mksoitex.F90)
  • Module mksrfdatMod (File: mksrfdatMod.F90)
    • mksrfdat
  • mkurban (File: mkurban.F90)
  • Module mpiinc (File: mpiinc.F90)
  • Module nanMod (File: nanMod.F90)
  • Module ncdioMod (File: ncdio.F90)
    • check_dim
    • check_var
    • check_ret
    • ncd_defvar
    • ncd_iolocal_int_1d
    • ncd_iolocal_real_1d
    • ncd_iolocal_int_2d
    • ncd_iolocal_real_2d
    • ncd_ioglobal_int_var
    • ncd_ioglobal_real_var
    • ncd_ioglobal_int_1d
    • ncd_ioglobal_real_1d
    • ncd_ioglobal_int_2d
    • ncd_ioglobal_real_2d
    • ncd_ioglobal_int_3d
    • ncd_ioglobal_real_3d
    • get_size_dim1
    • subroutine scam_field_offsets
  • Module pft2colMod (File: pft2colMod.F90)
    • pft2col
  • Module pftvarcon (File: pftvarcon.F90)
    • pftconrd
  • program_csm (File: program_csm.F90)
  • program_off (File: program_off.F90)
  • Module restFileMod (File: restFileMod.F90)
    • restart
    • restart_setup
    • restart_time
    • restart_biogeophys
    • restart_wrapup
    • write_rest_pfile
    • set_restart_filename
  • snowdp2lev (File: snowdp2lev.F90)
  • Module spmdGathScatMod (File: spmdGathScatMod.F90)
    • spmd_compute_mpigs
    • scatter_1darray_int
    • scatter_1darray_real
    • scatter_2darray_int
    • scatter_2darray_real
    • gather_1darray_int
    • gather_1darray_real
    • gather_2darray_int
    • gather_2darray_real
    • allgather_1darray_int
    • allgather_1darray_real
    • allgather_2darray_int
    • allgather_2darray_real
  • Module spmdMod (File: spmdMod.F90)
    • spmd_init
  • Module subgridAveMod (File: subgridAveMod.F90)
    • p2c_1d
    • p2c_2d
    • p2c_1d_filter
    • p2c_2d_filter
    • p2l_1d
    • p2l_2d
    • p2g_1d
    • p2g_2d
    • c2l_1d
    • c2l_2d
    • c2g_1d
    • c2g_2d
    • l2g_1d
    • l2g_2d
  • Module surfFileMod (File: surfFileMod.F90)
    • surfrd
  • system_cmd (File: system_cmd.c)
  • Module system_messages (File: system_messages.F90)
    • allocation_err
    • netcdf_err
    • iobin_err
  • Module time_manager (File: time_manager.F90)
    • timemgr_init
    • timemgr_restart
    • timemgr_print
    • advance_timestep
    • get_step_size
    • get_nstep
    • get_curr_date
    • get_prev_date
    • get_start_date
    • get_ref_date
    • get_curr_time
    • get_curr_calday
    • is_end_curr_day
    • is_end_curr_month
    • is_first_step
    • is_first_restart_step
    • is_last_step
    • timemgr_write_restart
    • timemgr_read_restart
    • chkrc
    • to_upper
  
  
• Index
• About this document ...