wip - Allow polygonal landunits to be initiated from surface file

Updates initialization routines to allow for polygonal landunits
to be created from namelist option and from polygon type
percentages specified on input file. In particular,
it allows for four landunits to be created with istsoil ltype
on each topounit so that the ice wedge polygons can have their
own soil columns as well as be vegetated. The fourth landunit
is for non-polygonal natural vegetated ground on the same topounit.

Author: rfiorella

components/elm/bld/namelist_files/namelist_defaults.xml

@@ -2155,4 +2155,7 @@ this mask will have smb calculated over the entire global land surface
 <use_fan use_fates=".true." >.false.</use_fan>
 <use_fan fan_mode='disable'>.false.</use_fan>
 
+<!-- NGEE Arctic Options -->
+<use_polygonal_tundra>.false.</use_polygonal_tundra>;
+
 </namelist_defaults>

components/elm/bld/namelist_files/namelist_definition.xml

@@ -2135,4 +2135,14 @@ not be called.
 <default>Default: 0</default>
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- NGEE Arctic Options                                                                       -->
+<!-- ========================================================================================  -->
+
+<entry id="use_polygonal_tundra" type="logical" category="default_settings"
+	group="elm_inparm" value=".false.">
+Use polygonal tundra parameterizations for ice wedge polygon microtopography and inindation fraction
+<default>Default: .false.</default>
+</entry>
+
 </namelist_definition>

components/elm/src/main/controlMod.F90

@@ -60,12 +60,12 @@ module controlMod
   ! !PUBLIC TYPES:
   implicit none
   save
-  
+
   ! !PUBLIC MEMBER FUNCTIONS:
   public :: control_setNL ! Set namelist filename
   public :: control_init  ! initial run control information
   public :: control_print ! print run control information
-  
+
   ! !PRIVATE TYPES:
   character(len=  7) :: runtyp(4)                        ! run type
   character(len=SHR_KIND_CL) :: NLFilename = 'lnd.stdin' ! Namelist filename
@@ -79,14 +79,14 @@ module controlMod
 
   !------------------------------------------------------------------------
   subroutine control_setNL( NLfile )
-    
+
     ! !DESCRIPTION:
     ! Set the namelist filename to use
-    
+
     ! !ARGUMENTS:
     implicit none
     character(len=*), intent(IN) :: NLFile ! Namelist filename
-    
+
     ! !LOCAL VARIABLES:
     character(len=32) :: subname = 'control_setNL'  ! subroutine name
     logical :: lexist                               ! File exists
@@ -111,19 +111,19 @@ end subroutine control_setNL
 
   !------------------------------------------------------------------------
   subroutine control_init( )
-    
+
     ! !DESCRIPTION:
     ! Initialize CLM run control information
-    
+
     ! !USES:
     use elm_time_manager          , only : set_timemgr_init, get_timemgr_defaults
     use fileutils                 , only : getavu, relavu
     use shr_string_mod            , only : shr_string_getParentDir
     use elm_interface_pflotranMod , only : elm_pf_readnl
     use ELMBeTRNLMod              , only : betr_readNL
-    
+
     implicit none
-    
+
     ! !LOCAL VARIABLES:
     character(len=32)  :: starttype ! infodata start type
     integer :: i,j,n                ! loop indices
@@ -306,8 +306,8 @@ subroutine control_init( )
     namelist /elm_inparm/ &
          do_budgets, budget_inst, budget_daily, budget_month, &
          budget_ann, budget_ltann, budget_ltend
- 
-    namelist /elm_inparm/ & 
+
+    namelist /elm_inparm/ &
          use_atm_downscaling_to_topunit, precip_downscaling_method
 
     namelist /elm_inparm/ &
@@ -318,16 +318,19 @@ subroutine control_init( )
 
     namelist /elm_mosart/ &
          lnd_rof_coupling_nstep
-		 
+
+    namelist /elm_inparm/ &
+         snow_shape, snicar_atm_type, use_dust_snow_internal_mixing
+
     namelist /elm_inparm/ &
-         snow_shape, snicar_atm_type, use_dust_snow_internal_mixing 
-    
-    namelist /elm_inparm/ & 
          use_modified_infil
 
     namelist /elm_inparm/ &
          use_fan, fan_mode, fan_to_bgc_veg, nh4_ads_coef
 
+   ! NGEE Arctic options
+   namelist /elm_inparm/ &
+         use_polygonal_tundra
     ! ----------------------------------------------------------------------
     ! Default values
     ! ----------------------------------------------------------------------
@@ -506,7 +509,7 @@ subroutine control_init( )
           end if
        end if
 
-       if (use_lch4 .and. use_vertsoilc) then 
+       if (use_lch4 .and. use_vertsoilc) then
           anoxia = .true.
        else
           anoxia = .false.
@@ -551,7 +554,7 @@ subroutine control_init( )
        if (use_lnd_rof_two_way) then
           if (lnd_rof_coupling_nstep < 1) then
           call endrun(msg=' ERROR: lnd_rof_coupling_nstep cannot be smaller than 1.'//&
-                   errMsg(__FILE__, __LINE__))     
+                   errMsg(__FILE__, __LINE__))
           endif
        endif
 
@@ -686,7 +689,7 @@ end subroutine control_init
 
   !------------------------------------------------------------------------
   subroutine control_spmd()
-    
+
     ! !DESCRIPTION:
     ! Distribute namelist data all processors. All program i/o is
     ! funnelled through the master processor. Processor 0 either
@@ -695,13 +698,13 @@ subroutine control_spmd()
     ! all processors and writes it to disk.
     !
     ! !USES:
-    
+
     use spmdMod,    only : mpicom, MPI_CHARACTER, MPI_INTEGER, MPI_LOGICAL, MPI_REAL8
     use elm_varpar, only : numrad
-    
+
     ! !ARGUMENTS:
     implicit none
-    
+
     ! !LOCAL VARIABLES:
     integer ier       !error code
     !-----------------------------------------------------------------------
@@ -874,7 +877,7 @@ subroutine control_spmd()
     call mpi_bcast (more_vertlayers,1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (const_climate_hist, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_top_solar_rad, 1, MPI_LOGICAL, 0, mpicom, ier)  ! TOP solar radiation parameterization
-    
+
     ! glacier_mec variables
     call mpi_bcast (create_glacier_mec_landunit, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (maxpatch_glcmec, 1, MPI_INTEGER, 0, mpicom, ier)
@@ -948,11 +951,11 @@ subroutine control_spmd()
 
     ! PETSc-based thermal model
     call mpi_bcast (use_petsc_thermal_model, 1, MPI_LOGICAL, 0, mpicom, ier)
-    
+
     ! Downscaling of atmospheric forcing to topounits
     call mpi_bcast (use_atm_downscaling_to_topunit, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (precip_downscaling_method, len(precip_downscaling_method), MPI_CHARACTER, 0, mpicom, ier)
-    
+
     ! soil erosion
     call mpi_bcast (use_erosion, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (ero_ccycle , 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -974,28 +977,30 @@ subroutine control_spmd()
     call mpi_bcast (snow_shape, len(snow_shape), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (snicar_atm_type, len(snicar_atm_type), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (use_dust_snow_internal_mixing, 1, MPI_LOGICAL, 0, mpicom, ier)
-	
+
     call mpi_bcast (mpi_sync_nstep_freq, 1, MPI_INTEGER, 0, mpicom, ier)
-    
+
     ! use modified infiltration scheme in surface water storage
     call mpi_bcast (use_modified_infil, 1, MPI_LOGICAL, 0, mpicom, ier)
 
+    !NGEE Arctic options
+    call mpi_bcast (use_polygonal_tundra, 1, MPI_LOGICAL, 0, mpicom, ier)
   end subroutine control_spmd
 
   !------------------------------------------------------------------------
   subroutine control_print ()
-    
+
     ! !DESCRIPTION:
     ! Write out the clm namelist run control variables
-    
+
     ! !USES:
-    
+
     use AllocationMod, only : suplnitro, suplnNon
     use AllocationMod, only : suplphos, suplpNon
-    
+
     ! !ARGUMENTS:
     implicit none
-    
+
     ! !LOCAL VARIABLES:
     integer i  !loop index
     character(len=32) :: subname = 'control_print'  ! subroutine name
@@ -1035,7 +1040,7 @@ subroutine control_print ()
     write(iulog,*) '    precip_downscaling_method = ', precip_downscaling_method
     write(iulog,*) 'input data files:'
     write(iulog,*) '   PFT physiology and parameters file = ',trim(paramfile)
-    write(iulog,*) '   Soil order dependent parameters file = ',trim(fsoilordercon)    
+    write(iulog,*) '   Soil order dependent parameters file = ',trim(fsoilordercon)
     if (fsurdat == ' ') then
        write(iulog,*) '   fsurdat, surface dataset not set'
     else
@@ -1056,13 +1061,13 @@ subroutine control_print ()
     else
        write(iulog,*) '   atm topographic data = ',trim(fatmtopo)
     end if
-    
+
     if (use_top_solar_rad) then
         write(iulog,*) '  use TOP solar radiation parameterization instead of PP'
     else
         write(iulog,*) '   use_top_solar_rad is False, so do not run TOP solar radiation parameterization'
     end if
-    
+
     if (use_cn) then
        if (suplnitro /= suplnNon)then
           write(iulog,*) '   Supplemental Nitrogen mode is set to run over Patches: ', &
@@ -1176,9 +1181,9 @@ subroutine control_print ()
     write(iulog,*) '   atm_gustiness   = ', atm_gustiness
     write(iulog,*) '   force_land_gustiness   = ', force_land_gustiness
     write(iulog,*) '   more vertical layers = ', more_vertlayers
-    
+
     write(iulog,*) '   Sub-grid topographic effects on solar radiation   = ', use_top_solar_rad  ! TOP solar radiation parameterization
-     
+
     if (nsrest == nsrContinue) then
        write(iulog,*) 'restart warning:'
        write(iulog,*) '   Namelist not checked for agreement with initial run.'
@@ -1241,9 +1246,9 @@ subroutine control_print ()
     write(iulog,*) '    use_lnd_rof_two_way    = ', use_lnd_rof_two_way
     write(iulog,*) '    lnd_rof_coupling_nstep = ', lnd_rof_coupling_nstep
     write(iulog,*) '    mpi_sync_nstep_freq    = ', mpi_sync_nstep_freq
-    
+
     write(iulog,*) '    use_modified_infil = ', use_modified_infil
-    
+
 
    ! FAN
     write(iulog,*) '    use_fan                = ', use_fan
@@ -1253,6 +1258,8 @@ subroutine control_print ()
        write(iulog,*) ' fan_to_bgc_veg = ', fan_to_bgc_veg
     end if
 
+    ! NGEE Arctic options
+    if (use_polygonal_tundra) write(iulog, *) '    use_polygonal_tundra    =', use_polygonal_tundra
   end subroutine control_print
 
 end module controlMod

components/elm/src/main/elm_varctl.F90

@@ -374,7 +374,11 @@ module elm_varctl
   logical, public :: fan_nh3_to_atm      = .false.
   logical, public :: fan_to_bgc_crop     = .false.
   logical, public :: fan_to_bgc_veg      = .false.
- 
+
+  !----------------------------------------------------------
+  ! NGEE Arctic parameterizations
+  !----------------------------------------------------------
+  logical, public :: use_polygonal_tundra = .false.
 
   !----------------------------------------------------------
   ! VSFM switches
@@ -524,8 +528,8 @@ module elm_varctl
    !----------------------------------------------------------
    logical, public :: use_lnd_rof_two_way = .false.
    integer, public :: lnd_rof_coupling_nstep = 0
-   
-   
+
+
    !----------------------------------------------------------
    ! SNICAR-AD
    !----------------------------------------------------------
@@ -537,7 +541,7 @@ module elm_varctl
    ! MPI syncing
    !----------------------------------------------------------
    integer, public :: mpi_sync_nstep_freq = 0
-   
+
    !----------------------------------------------------------
    ! Modified infiltration scheme in surface water storage
    !----------------------------------------------------------

components/elm/src/main/elm_varsur.F90

@@ -2,7 +2,7 @@ module elm_varsur
 
   !-----------------------------------------------------------------------
   ! Module containing 2-d surface boundary data information
-  ! surface boundary data, these are all "gdc" local 
+  ! surface boundary data, these are all "gdc" local
   ! Note that some of these need to be pointers (as opposed to just allocatable arrays) to
   ! match the ncd_io interface; for consistency, we make them all pointers
   !
@@ -14,20 +14,26 @@ module elm_varsur
   save
   !
   ! weight of each landunit on the topounit in the grid cell
-  real(r8), pointer :: wt_lunit(:,:,:)    
+  real(r8), pointer :: wt_lunit(:,:,:)
 
   ! whether we have valid urban data in each grid cell or (in each topounit)
   logical , pointer :: urban_valid(:,:)
 
   ! for natural veg landunit, weight of each pft on the landunit (adds to 1.0 on the
   ! landunit for all all grid cells, even! those without any natural pft)
   ! (second dimension goes natpft_lb:natpft_ub)
-  real(r8), pointer :: wt_nat_patch(:,:,:)   
+  real(r8), pointer :: wt_nat_patch(:,:,:)
+
+  ! for polygonal tundra special case of natural veg landunit, weight of polygon type
+  ! with respect to the natural vegetation landunit (NOT the grid cell). these do
+  ! not need to sum to 1 to preserve possibility of polygonal tundra and non-polygonal
+  ! ground on the same grid cell, on the vegetated landunit.
+  real(r8), pointer :: wt_polygon(:,:,:) ! dims: clump, topounit, polygon type
 
   ! for crop landunit, weight of each cft on the landunit (adds to 1.0 on the
   ! landunit for all all grid cells, even  those without any crop)
   ! (second dimension goes cft_lb:cft_ub)
-  real(r8), pointer :: wt_cft(:,:,:)       
+  real(r8), pointer :: wt_cft(:,:,:)
 
   ! for each cft on the crop landunit prescribe annual fertilizer
   ! landunit for all all grid cells, even  those without any crop)
@@ -37,19 +43,19 @@ module elm_varsur
 
   ! for glc_mec landunits, weight of glacier in each elevation class (adds to 1.0 on the
   ! landunit for all grid cells, even those without any glacier)
-  real(r8), pointer :: wt_glc_mec(:,:,:)   
+  real(r8), pointer :: wt_glc_mec(:,:,:)
 
   ! subgrid glacier_mec sfc elevation
-  real(r8), pointer :: topo_glc_mec(:,:,:) 
-  
+  real(r8), pointer :: topo_glc_mec(:,:,:)
+
   ! Topounit related poiters
   real(r8), pointer :: num_tunit_per_grd(:)   ! Topounit area fraction
   real(r8), pointer :: wt_tunit(:,:)   ! Topounit area fraction
-  real(r8), pointer :: elv_tunit(:,:)  ! Topounit elevation 
-  real(r8), pointer :: slp_tunit(:,:)  ! Topounit slope 
+  real(r8), pointer :: elv_tunit(:,:)  ! Topounit elevation
+  real(r8), pointer :: slp_tunit(:,:)  ! Topounit slope
   integer, pointer :: asp_tunit(:,:)  ! Topounit aspect
-  
-  real(r8),pointer :: firrig(:,:) 
+
+  real(r8),pointer :: firrig(:,:)
   real(r8),pointer :: f_surf(:,:)  ! fraction of water withdraws from surfacewater
   real(r8),pointer :: f_grd(:,:)   ! fraction of water withdraws from groundwater
   !-----------------------------------------------------------------------