379 updated branch with all GW changes

CMakeLists.txt

@@ -36,11 +36,11 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
         "$<$<CONFIG:Debug>:${CABLE_GNU_Fortran_FLAGS_DEBUG}>"
     )
 endif()
-
+set(CMAKE_Fortran_MODULE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/include")
 if(CABLE_LIBRARY)
 
     add_library(
-        cable_science
+        cable
         STATIC
         src/science/albedo/cbl_albedo.F90
         src/science/albedo/cbl_snow_albedo.F90
@@ -70,18 +70,18 @@ if(CABLE_LIBRARY)
         src/science/casa-cnp/casa_rplant.F90
         src/science/casa-cnp/casa_sumcflux.F90
         src/science/casa-cnp/casa_variable.F90
-        src/science/gw_hydro/cable_gw_hydro.F90
-        src/science/gw_hydro/cable_psm.F90
+        #src/science/gw_hydro/cable_gw_hydro.F90
+        #src/science/gw_hydro/cable_psm.F90
         src/science/landuse/landuse3.F90
         src/science/landuse/landuse_constant.F90
         src/science/misc/cable_air.F90
         src/science/misc/cable_carbon.F90
         src/science/misc/cable_climate.F90
         src/science/pop/pop_constants.F90
         src/science/pop/pop_def.F90
-        src/science/pop/POP.F90
-        src/science/pop/pop_io.F90
-        src/science/pop/POPLUC.F90
+        #src/science/pop/POP.F90
+        #src/science/pop/pop_io.F90
+        #src/science/pop/POPLUC.F90
         src/science/pop/pop_types.F90
         src/science/radiation/cbl_init_radiation.F90
         src/science/radiation/cbl_radiation.F90
@@ -90,11 +90,11 @@ if(CABLE_LIBRARY)
         src/science/radiation/cbl_spitter.F90
         src/science/roughness/cable_roughness.F90
         src/science/roughness/roughnessHGT_effLAI_cbl.F90
-        src/science/sli/cable_sli_main.F90
-        src/science/sli/cable_sli_numbers.F90
-        src/science/sli/cable_sli_roots.F90
-        src/science/sli/cable_sli_solve.F90
-        src/science/sli/cable_sli_utils.F90
+        #src/science/sli/cable_sli_main.F90
+        #src/science/sli/cable_sli_numbers.F90
+        #src/science/sli/cable_sli_roots.F90
+        #src/science/sli/cable_sli_solve.F90
+        #src/science/sli/cable_sli_utils.F90
         src/science/soilsnow/cbl_conductivity.F90
         src/science/soilsnow/cbl_GW.F90
         src/science/soilsnow/cbl_hyd_redistrib.F90
@@ -122,14 +122,33 @@ if(CABLE_LIBRARY)
         src/params/cable_maths_constants_mod.F90
         src/util/cable_runtime_opts_mod.F90
         src/util/cable_common.F90
-        src/coupled/esm16/casa_offline_inout.F90
-        src/coupled/esm16/casa_ncdf.F90
-        src/coupled/esm16/cable_iovars.F90
-        src/coupled/esm16/cable_surface_types.F90
-        src/coupled/esm16/cable_define_types.F90
-        src/coupled/esm16/cable_phenology.F90
-        src/coupled/esm16/cable_LUC_EXPT.F90
+        src/coupled/esm/cable_iovars.F90
+        src/coupled/esm/cable_surface_types.F90
+        src/coupled/esm/cable_define_types.F90
+        src/coupled/esm/cable_soil_params_mod.F90
+        src/coupled/esm/cable_pft_params_mod.F90
+        src/coupled/esm/casa_landuse.F90
+        src/coupled/esm/LAI_canopy_height_cbl.F90
+        #src/shared/casa_offline_inout.F90
+        #src/shared/casa_ncdf.F90
+        #src/shared/cable_phenology.F90
+        #src/shared/cable_LUC_EXPT.F90
+        src/coupled/shared/cable_canopy_type_mod.F90
+        src/coupled/shared/cable_soilsnow_type_mod.F90
+        src/coupled/shared/cable_soil_type_mod.F90
+        src/coupled/shared/cable_veg_type_mod.F90
+        src/util/cable_climate_type_mod.F90
+        src/util/masks_cbl.F90
     )
+    target_compile_definitions(cable PRIVATE UM_CBL)
+    target_include_directories(cable PUBLIC "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
+
+    install(TARGETS cable
+      EXPORT CABLEFortranTargets
+      LIBRARY DESTINATION lib
+      INCLUDES DESTINATION include)
+
+    install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/ TYPE INCLUDE)
 
 else()
 

build.bash

@@ -62,7 +62,7 @@ while [ ${#} -gt 0 ]; do
             cmake_args+=(-DCABLE_MPI="ON")
             ;;
         -l|--library)
-            build_args+=(--target cable_science)
+            build_args+=(--target cable)
             cmake_args+=(-DCABLE_LIBRARY="ON")
             do_install=0 # Disable installation when only building the science library
             ;;

documentation/docs/developer_guide/documentation_guidelines/index.md

@@ -29,5 +29,5 @@ To help you find the file corresponding to a page, on the rendered [documentatio
 [cheat-sheets]: ../other_resources/cheat_sheets.md
 [api-guidelines]: science_doc.md
 [doc-pages]: https://cable.readthedocs.io/en/latest
-[Hive-contribute]: https://access-hive.org.au/about/contribute/
+[Hive-contribute]: https://docs.access-hive.org.au/about/contribute/
 [cable-lsm-join]: https://github.com/CABLE-LSM/CABLE/issues/110

src/coupled/AM3/control/cable/CM3/cbl_canopy_type.F90

@@ -63,7 +63,6 @@ MODULE cable_canopy_type_mod
   REAL, ALLOCATABLE, PUBLIC :: fwet(:)              ! fraction of canopy wet
   REAL, ALLOCATABLE, PUBLIC :: fns_cor(:)           ! correction to net rad avail to soil (W/m2)
   REAL, ALLOCATABLE, PUBLIC :: ga_cor(:)            ! correction to ground heat flux (W/m2)    
-  REAL, ALLOCATABLE, PUBLIC :: evapfbl(:,:)         ! 
   REAL, ALLOCATABLE, PUBLIC :: gswx(:,:)            ! stom cond for water
   REAL, ALLOCATABLE, PUBLIC :: zetar(:,:)           ! stability parameter (ref height)
   REAL, ALLOCATABLE, PUBLIC :: zetash(:,:)          ! stability parameter (shear height)
@@ -144,7 +143,6 @@ MODULE cable_canopy_type_mod
   REAL, POINTER, PUBLIC :: fwet(:)              ! fraction of canopy wet
   REAL, POINTER, PUBLIC :: fns_cor(:)           ! correction to net rad avail to soil (W/m2)
   REAL, POINTER, PUBLIC :: ga_cor(:)            ! correction to ground heat flux (W/m2)    
-  REAL, POINTER, PUBLIC :: evapfbl(:,:)         ! 
   REAL, POINTER, PUBLIC :: gswx(:,:)            ! stom cond for water
   REAL, POINTER, PUBLIC :: zetar(:,:)           ! stability parameter (ref height)
   REAL, POINTER, PUBLIC :: zetash(:,:)          ! stability parameter (shear height)
@@ -230,7 +228,6 @@ SUBROUTINE alloc_canopy_type(var, mp)
 ALLOCATE( var% fwet(mp) )
 ALLOCATE( var% fns_cor(mp) )    !REV_CORR variable
 ALLOCATE( var% ga_cor(mp) )     !REV_CORR variable
-ALLOCATE( var % evapfbl(mp,nsl) )
 ALLOCATE( var% epot(mp) )
 ALLOCATE( var% fnpp(mp) )
 ALLOCATE( var% fevw_pot(mp) )
@@ -308,7 +305,6 @@ SUBROUTINE alloc_canopy_type(var, mp)
 var % fwet(:)        = 0.0      
 var % fns_cor(:)     = 0.0      
 var % ga_cor(:)      = 0.0      
-var % evapfbl(:,:)   = 0.0      
 var % gswx(:,:)      = 0.0      
 var % zetar(:,:)     = 0.0      
 var % zetash(:,:)    = 0.0      
@@ -382,7 +378,6 @@ SUBROUTINE dealloc_canopy_type(var)
    DEALLOCATE( var% fwet )
    DEALLOCATE( var% fns_cor )   !REV_CORR variable
    DEALLOCATE( var% ga_cor )    !REV_CORR variable
-   DEALLOCATE ( var % evapfbl )
    DEALLOCATE( var% epot )
    DEALLOCATE( var% fnpp )
    DEALLOCATE( var% fevw_pot )
@@ -473,7 +468,6 @@ SUBROUTINE assoc_canopy_type(canopy, canopy_data )
 canopy% fwet        => canopy_data% fwet
 canopy% fns_cor     => canopy_data% fns_cor
 canopy% ga_cor      => canopy_data% ga_cor
-canopy% evapfbl     => canopy_data% evapfbl
 canopy% gswx        => canopy_data% gswx
 canopy% zetar       => canopy_data% zetar
 canopy% zetash      => canopy_data% zetash
@@ -557,7 +551,6 @@ SUBROUTINE nullify_canopy_cbl( var )
    NULLIFY( var% fwet )
    NULLIFY( var% fns_cor )   !REV_CORR variable
    NULLIFY( var% ga_cor )    !REV_CORR variable
-   NULLIFY( var % evapfbl )
    NULLIFY( var% epot )
    NULLIFY( var% fnpp )
    NULLIFY( var% fevw_pot )

src/coupled/AM3/control/cable/CM3/ssnow_type.F90

@@ -74,11 +74,11 @@ MODULE cable_soil_snow_type_mod
   REAL, ALLOCATABLE :: tggsn        (:,:) ! snow temperature in K
   REAL, ALLOCATABLE :: dtmlt        (:,:) ! water flux to the soil
   REAL, ALLOCATABLE :: albsoilsn    (:,:) ! soil + snow reflectance
-  REAL, ALLOCATABLE :: evapfbl      (:,:) !
   REAL, ALLOCATABLE :: tilefrac     (:,:) ! factor for latent heat
 
   REAL(r_2), ALLOCATABLE :: wbtot      (:) ! total soil water (mm) 
 
+  REAL(r_2), ALLOCATABLE :: evapfbl     (:,:) !
   REAL(r_2), ALLOCATABLE :: gammzz      (:,:) ! heat capacity for each soil layer
   REAL(r_2), ALLOCATABLE :: wb          (:,:) ! volumetric soil moisture (solid+liq)
   REAL(r_2), ALLOCATABLE :: wbice       (:,:) ! soil ice 
@@ -209,11 +209,11 @@ MODULE cable_soil_snow_type_mod
   REAL, POINTER :: tggsn        (:,:) ! snow temperature in K
   REAL, POINTER :: dtmlt        (:,:) ! water flux to the soil
   REAL, POINTER :: albsoilsn    (:,:) ! soil + snow reflectance
-  REAL, POINTER :: evapfbl      (:,:) !
   REAL, POINTER :: tilefrac     (:,:) ! factor for latent heat
 
   REAL(r_2), POINTER :: wbtot      (:) ! total soil water (mm) 
 
+  REAL(r_2), POINTER :: evapfbl     (:,:) !
   REAL(r_2), POINTER :: gammzz      (:,:) ! heat capacity for each soil layer
   REAL(r_2), POINTER :: wb          (:,:) ! volumetric soil moisture (solid+liq)
   REAL(r_2), POINTER :: wbice       (:,:) ! soil ice 

src/coupled/esm/LAI_canopy_height_cbl.F90

@@ -0,0 +1,156 @@
+!******************************COPYRIGHT********************************************
+! (c) CSIRO 2022.
+! All rights reserved.
+!
+! This routine has been licensed to the other JULES partners for use and
+! distribution under the JULES collaboration agreement, subject to the terms and
+! conditions set out therein.
+!
+! [Met Office Ref SC0237]
+!******************************COPYRIGHT********************************************
+MODULE cbl_LAI_canopy_height_mod
+
+!-----------------------------------------------------------------------------
+! Description:
+!   Restricts the range of canopy height and LAI inherited from JULES/UM
+!   spatial maps
+!
+! This MODULE is USEd by:
+!      cable_land_albedo_mod_cbl.F90
+!
+! This MODULE contains 1 public Subroutine:
+!      limit_HGT_LAI
+!
+! Code Owner: Please refer to ModuleLeaders.txt
+! This file belongs in CABLE SCIENCE
+!
+! Code Description:
+!   Language: Fortran 90.
+!   This code is written to JULES coding standards v1.
+!-----------------------------------------------------------------------------
+
+IMPLICIT NONE
+PUBLIC :: limit_HGT_LAI
+PRIVATE
+
+CONTAINS
+
+SUBROUTINE Limit_HGT_LAI( HGT_pft_temp, LAI_pft_cbl, HGT_pft_cbl, mp, land_pts,&
+                          ntiles, npft, tile_pts, tile_index, tile_frac,       &
+                          L_tile_pts, LAI_pft, HGT_pft, CLAI_thresh )
+
+!*## Purpose
+!
+! This SUBROUTINE checks that input values of leaf area and canopy height
+! lie between set values (defined by PFT) and overwrites if necessary.
+! These limits are needed to ensure that the canopy roughness properties of
+! the land point are well behaved (see [[ruff_resist]]).
+!
+! The mapping from grid cells (land_pts,ntiles) to the (mp) structure
+! is also undertaken.
+!
+! **This SUBROUTINE is active when CABLE is run within a coupled model
+! (i.e. ACCESS)** 
+!
+!## Method
+!
+! The cell-level input (land_pts,ntile) variables for leaf area `LAI_pft` and
+! canopy height `HGT_pft` are checked for
+!
+! - whether the land_pt has a non-zero fraction of that tile (if zero
+!   fraction then LAI and canopy height are set to zero)
+! - whether the LAI lies above a minimum value `CLAI_thresh`
+! - whether the canopy height lies above a minimum value (which is PFT dependent)
+! - whether non-vegetated tiles have a non-zero canopy height.
+!
+! Outputs are `LAI_pft_cbl` and `HGT_pft_cbl`
+!
+! **WARNINGS**
+!
+! - INTENT statements need to be added to the argument lists
+! - hardwired indexing is used throughout.  This SUBROUTINE assumes that
+!     1. non-vegetated tiles take indexes 14 and onwards
+!     2. tall vegetation occupies tile indexes 1-4
+!     3. other vegetation (shrubs/grasses/crops/wetlands) occupy tile indexes
+!     5-13
+! - the limits on canopy height are hardwired
+!     1. canopy height for tall vegetation is limited to be greater than 1m
+!     2. canopy height for other vegetation is limited to be greater than 0.1m
+
+USE cable_surface_types_mod, ONLY: shrub_cable, evergreen_broadleaf,           &
+                                   deciduous_broadleaf, aust_temperate,        &       
+                                   aust_tropical        
+
+IMPLICIT NONE
+
+INTEGER, INTENT(IN)  :: land_pts, ntiles, npft        !! # land points here 
+                                                      !! max # of tiles, PFTs
+!! CABLE 1-D vector of length "mp" active tiles
+INTEGER, INTENT(IN)  :: mp                            !! total number of tiles 
+
+!! range limited LAI/ canopy height 
+REAL,    INTENT(OUT) :: HGT_pft_temp(land_pts,ntiles) !! UM dimensions (m)
+
+!! PACKed to  CABLE 1-D vector of length mp
+REAL,    INTENT(OUT) :: LAI_pft_cbl(mp)               !! veg%vlai 
+REAL,    INTENT(OUT) :: HGT_pft_cbl(mp)               !! veg%hc
+
+!! From UM spatial maps via restart or ancillary. 
+REAL,    INTENT(IN)  :: tile_frac(land_pts,ntiles)    !! frac. veg/non-veg type
+INTEGER, INTENT(IN)  :: tile_pts(ntiles)              !! # tiles per PFT type
+INTEGER, INTENT(IN)  :: tile_index(land_pts,ntiles)   !! land_pt index per tile
+!! updates monthly
+REAL,    INTENT(IN)  :: LAI_pft(land_pts, npft)       !! LAI (m\(^2\)m\(^{-2}\))
+REAL,    INTENT(IN)  :: HGT_pft(land_pts, npft)       !! canopy height (m)         
+!! logical mask. TRUE if tilefrac > 0 0 (OR some threshold)
+LOGICAL, INTENT(IN) :: L_tile_pts(land_pts,ntiles)
+
+!! scalar constant threshold for "cell" to be considred vegetated
+REAL,    INTENT(IN)  :: Clai_thresh                   ! minimum LAI threshold 
+
+!local vars
+INTEGER :: i,j, n
+REAL :: LAI_pft_temp(land_pts,ntiles) ! needed to filter spatail map
+
+!Retain init where tile_frac=0
+LAI_pft_temp(:,:) = 0.0
+HGT_pft_temp(:,:) = 0.0
+
+!Comensurate with restricted ordering of PFTs in UM. Not generically applicable 
+DO n=1,ntiles
+  DO j=1,tile_pts(n)
+
+    i = tile_index(j,n)  ! landpt index
+
+    IF( tile_frac(i,n) .GT. 0.0 ) THEN
+
+      IF( n < shrub_cable ) THEN ! trees 
+
+        LAI_pft_temp(i,n) = MAX( 0.99*CLAI_thresh, LAI_pft(i,n) )
+        HGT_pft_temp(i,n) = MAX( 1.0, HGT_pft(i,n) )
+
+      ELSE IF( n >= shrub_cable  .AND. n < aust_temperate ) THEN  ! shrubs/grass
+
+        LAI_pft_temp(i,n) = MAX( 0.99*CLAI_thresh, LAI_pft(i,n) )
+        HGT_pft_temp(i,n) = MAX( 0.1, HGT_pft(i,n) ) 
+
+      ELSE IF( n == aust_temperate .OR. n == aust_tropical ) THEN  ! Aust. trees
+
+        LAI_pft_temp(i,n) = MAX( CLAI_thresh, LAI_pft(i,n) ) 
+        HGT_pft_temp(i,n) = MAX( 1.0, HGT_pft(i,n) ) 
+
+      ENDIF
+
+    ENDIF
+
+  ENDDO
+ENDDO
+
+!surface_type = PACK(surface_type_temp, um1%L_TILE_PTS)
+LAI_pft_cbl  = PACK(LAI_pft_temp, l_tile_pts)
+HGT_pft_cbl  = PACK(HGT_pft_temp, l_tile_pts)
+
+END SUBROUTINE limit_HGT_LAI
+
+END MODULE cbl_LAI_canopy_height_mod
+

src/coupled/esm/cable_surface_types.F90

@@ -24,8 +24,8 @@ MODULE cable_surface_types_mod
   INTEGER, PARAMETER :: c3_cropland          = 9  
   INTEGER, PARAMETER :: c4_cropland          = 10 
   INTEGER, PARAMETER :: wetland              = 11 
-  INTEGER, PARAMETER :: empty1               = 12
-  INTEGER, PARAMETER :: empty2               = 13
+  INTEGER, PARAMETER :: aust_temperate       = 12
+  INTEGER, PARAMETER :: aust_tropical        = 13
   INTEGER, PARAMETER :: barren_cable         = 14
   INTEGER, PARAMETER :: urban_cable          = 15
   INTEGER, PARAMETER :: lakes_cable          = 16 

src/coupled/shared/cable_canopy_type_mod.F90

@@ -62,7 +62,6 @@ MODULE cable_canopy_type_mod
        ga_cor  ! correction to ground heat flux (W/m2)
 
   REAL, DIMENSION(:,:), POINTER ::                                            &
-       evapfbl,                                                               &
        gswx,    & ! stom cond for water
        zetar, &   ! stability parameter (ref height)
                              ! vh_js !
@@ -158,7 +157,6 @@ SUBROUTINE alloc_canopy_type(var, mp)
 ALLOCATE( var% fwet(mp) )
 ALLOCATE( var% fns_cor(mp) )    !REV_CORR variable
 ALLOCATE( var% ga_cor(mp) )     !REV_CORR variable
-ALLOCATE ( var % evapfbl(mp,ms) )
 ALLOCATE( var% epot(mp) )
 ALLOCATE( var% fnpp(mp) )
 ALLOCATE( var% fevw_pot(mp) )

src/coupled/shared/cable_soilsnow_type_mod.F90

@@ -72,14 +72,14 @@ MODULE cable_soil_snow_type_mod
        tggsn,      & ! snow temperature in K
        dtmlt,      & ! water flux to the soil
        albsoilsn,  & ! soil + snow reflectance
-       evapfbl,    & !
        tilefrac      ! factor for latent heat
 
 
   REAL(r_2), DIMENSION(:), POINTER ::                                         &
        wbtot   ! total soil water (mm)
 
   REAL(r_2), DIMENSION(:,:), POINTER ::                                       &
+       evapfbl,    & !
        gammzz,  & ! heat capacity for each soil layer
        wb,      & ! volumetric soil moisture (solid+liq)
        wbice,   & ! soil ice