Merge pull request #1 from billsacks/agsys

Organize agsys into 3 subdirectories

cime_config/buildlib

@@ -52,7 +52,9 @@ def _main_func():
                      os.path.join(lnd_root,"src","fates","biogeophys"),
                      os.path.join(lnd_root,"src","fates","biogeochem"),
                      os.path.join(lnd_root,"src","fates","fire"),
-                     os.path.join(lnd_root,"src","agsys"),
+                     os.path.join(lnd_root,"src","agsys","ctsm_interface"),
+                     os.path.join(lnd_root,"src","agsys","ctsm_wrappers"),
+                     os.path.join(lnd_root,"src","agsys","science"),
                      os.path.join(lnd_root,"src","utils"),
                      os.path.join(lnd_root,"src","cpl"),
                      os.path.join(lnd_root,"src","cpl",driver)]

src/agsys/AgSys.F90 → src/agsys/ctsm_interface/AgSys.F90

@@ -10,8 +10,9 @@ module AgSys
 #include "shr_assert.h"
   use clm_time_manager, only : is_beg_curr_day
   use decompMod, only : bounds_type
-  use AgSysCommon, only : agsys_common_type
+  use AgSysGeneral, only : agsys_general_type
   use AgSysParams, only : agsys_params_type
+  use AgSysParamReader, only : ReadParams
   use AgSysClimate, only : agsys_climate_type
   use AgSysPhenology, only : agsys_phenology_type
   !
@@ -22,7 +23,7 @@ module AgSys
 
   type, public :: agsys_type
      private
-     type(agsys_common_type)    :: agsys_common_inst
+     type(agsys_general_type)    :: agsys_general_inst
      type(agsys_params_type)    :: agsys_params_inst
      type(agsys_climate_type)   :: agsys_climate_inst
      type(agsys_phenology_type) :: agsys_phenology_inst
@@ -86,8 +87,8 @@ subroutine Init(this, bounds)
     character(len=*), parameter :: subname = 'Init'
     !-----------------------------------------------------------------------
 
-    call this%agsys_common_inst%Init(bounds)
-    call this%agsys_params_inst%Init()
+    call this%agsys_general_inst%Init(bounds)
+    call ReadParams(this%agsys_params_inst)
     call this%agsys_climate_inst%Init(bounds)
     call this%agsys_phenology_inst%Init(bounds)
 

src/agsys/AgSysCommon.F90 → src/agsys/ctsm_interface/AgSysGeneral.F90

@@ -1,8 +1,8 @@
-module AgSysCommon
+module AgSysGeneral
 
   !-----------------------------------------------------------------------
   ! !DESCRIPTION:
-  ! Class containing data used by multiple other AgSys classes
+  ! Class containing general data used by multiple other AgSys classes
   !
   ! !USES:
 #include "shr_assert.h"
@@ -15,19 +15,15 @@ module AgSysCommon
 
   ! !PUBLIC TYPES:
 
-  integer, parameter, public :: crop_type_maize = 1
-  integer, parameter, public :: crop_type_soybean = 2
-  integer, parameter, public :: crop_type_maxval = 2
-
-  type, public :: agsys_common_type
+  type, public :: agsys_general_type
      private
 
      ! ------------------------------------------------------------------------
      ! Public data members, time-constant
      ! ------------------------------------------------------------------------
 
-     ! AgSys's crop type: one of the crop_type_* constants defined above; note that these
-     ! may differ from the constants in pftconMod
+     ! AgSys's crop type: one of the crop_type_* constants defined in AgSysConstants; note
+     ! that these may differ from the constants in pftconMod
      integer, pointer, public :: crop_type_patch(:)
 
      ! Cultivar type. A given value implies a given crop type; for example, cultivar
@@ -52,7 +48,7 @@ module AgSysCommon
    contains
      procedure, public :: Init
      procedure, private :: InitAllocate
-  end type agsys_common_type
+  end type agsys_general_type
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -63,10 +59,10 @@ module AgSysCommon
   subroutine Init(this, bounds)
     !
     ! !DESCRIPTION:
-    ! Initialize this agsys_common_type instance
+    ! Initialize this agsys_general_type instance
     !
     ! !ARGUMENTS:
-    class(agsys_common_type), intent(inout) :: this
+    class(agsys_general_type), intent(inout) :: this
     type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
@@ -81,10 +77,10 @@ end subroutine Init
   subroutine InitAllocate(this, bounds)
     !
     ! !DESCRIPTION:
-    ! Allocate components of this agsys_common_type instance
+    ! Allocate components of this agsys_general_type instance
     !
     ! !ARGUMENTS:
-    class(agsys_common_type), intent(inout) :: this
+    class(agsys_general_type), intent(inout) :: this
     type(bounds_type), intent(in) :: bounds
     !
     ! !LOCAL VARIABLES:
@@ -105,4 +101,4 @@ subroutine InitAllocate(this, bounds)
     end associate
   end subroutine InitAllocate
 
-end module AgSysCommon
+end module AgSysGeneral

src/agsys/ctsm_interface/AgSysParamReader.F90

@@ -0,0 +1,40 @@
+module AgSysParamReader
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Routines for reading AgSys's time-constant parameters
+  !
+  ! !USES:
+#include "shr_assert.h"
+  use shr_kind_mod     , only : r8 => shr_kind_r8
+  use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
+  use AgSysParams      , only : agsys_params_type
+  !
+  implicit none
+  private
+
+  ! !PUBLIC ROUTINES:
+  public :: ReadParams
+
+  character(len=*), parameter, private :: sourcefile = &
+       __FILE__
+
+contains
+
+  !-----------------------------------------------------------------------
+  subroutine ReadParams(params)
+    !
+    ! !DESCRIPTION:
+    ! Read parameters
+    !
+    ! !ARGUMENTS:
+    type(agsys_params_type), intent(inout) :: params
+    !
+    ! !LOCAL VARIABLES:
+
+    character(len=*), parameter :: subname = 'ReadParams'
+    !-----------------------------------------------------------------------
+
+  end subroutine ReadParams
+
+end module AgSysParamReader

src/agsys/ctsm_interface/README

@@ -0,0 +1,3 @@
+This directory contains modules that are specific to the CTSM
+implementation of AgSys. Furthermore, CTSM should only interact with
+AgSys via the modules here.

src/agsys/ctsm_wrappers/AgSysKinds.F90

@@ -0,0 +1,17 @@
+module AgSysKinds
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Kind parameters needed by AgSys
+  !
+  ! !USES:
+  use shr_kind_mod , only : r8 => shr_kind_r8
+  !
+  implicit none
+  private
+
+  ! !PUBLIC DATA:
+
+  public :: r8  ! imported from shr_kind_mod
+
+end module AgSysKinds

src/agsys/ctsm_wrappers/README

@@ -0,0 +1,7 @@
+The modules here provide wrappers to constants, variables and low-level
+routines in CTSM that are used by the AgSys science code in order to
+make it operate consistently with the rest of CTSM. If AgSys were
+plugged in to a different land model, the code in this directory would
+need to be replaced by alternatives that provided the same interface but
+referenced constants, variables and routines that are available in the
+given host model.

src/agsys/science/AgSysConstants.F90

@@ -0,0 +1,20 @@
+module AgSysConstants
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Constants needed throughout AgSys
+  !
+  ! !USES:
+
+  !
+  implicit none
+  private
+
+  ! !PUBLIC DATA:
+
+  ! Crop types
+  integer, parameter, public :: crop_type_maize = 1
+  integer, parameter, public :: crop_type_soybean = 2
+  integer, parameter, public :: crop_type_maxval = 2
+
+end module AgSysConstants

src/agsys/science/AgSysParams.F90

@@ -0,0 +1,26 @@
+module AgSysParams
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Derived type holding AgSys's time-constant parameters, defining various crops and
+  ! cultivars
+  !
+  ! Variables with suffix '_crop' are indexed by crop_type; variables with suffix
+  ! '_cultivar' are indexed by cultivar.
+  !
+  ! !USES:
+  use AgSysKinds, only : r8
+  !
+  implicit none
+  private
+
+  ! !PUBLIC TYPES:
+  type, public :: agsys_params_type
+     private
+
+     ! Public data members
+     real(r8), allocatable, public :: shoot_lag_cultivar(:)
+     real(r8), allocatable, public :: shoot_rate_cultivar(:)
+  end type agsys_params_type
+
+end module AgSysParams

src/agsys/science/README

@@ -0,0 +1,7 @@
+This directory contains the science implementation of AgSys. Modules
+here should not depend on CTSM data structures or routines, so that this
+directory could be copied in its entirety into another land model. The
+only dependencies should be on (1) other modules in this directory, and
+(2) modules in the ctsm_wrappers subdirectory. The latter would be
+replaced by a different set of wrappers if AgSys were imported into a
+different land model.