Merge pull request #2 from billsacks/agsys

Add agsys_phases_type and accumulated_thermal_time_phases

src/agsys/ctsm_interface/AgSys.F90

@@ -12,7 +12,8 @@ module AgSys
   use decompMod, only : bounds_type
   use AgSysGeneral, only : agsys_general_type
   use AgSysParams, only : agsys_params_type
-  use AgSysParamReader, only : ReadParams
+  use AgSysPhases, only : agsys_phases_type
+  use AgSysParamReader, only : ReadParams, ReadPhases
   use AgSysClimate, only : agsys_climate_type
   use AgSysPhenology, only : agsys_phenology_type
   !
@@ -23,8 +24,9 @@ module AgSys
 
   type, public :: agsys_type
      private
-     type(agsys_general_type)    :: agsys_general_inst
+     type(agsys_general_type)   :: agsys_general_inst
      type(agsys_params_type)    :: agsys_params_inst
+     type(agsys_phases_type)    :: agsys_phases_inst
      type(agsys_climate_type)   :: agsys_climate_inst
      type(agsys_phenology_type) :: agsys_phenology_inst
 
@@ -89,7 +91,8 @@ subroutine Init(this, bounds)
 
     call this%agsys_general_inst%Init(bounds)
     call ReadParams(this%agsys_params_inst)
-    call this%agsys_climate_inst%Init(bounds)
+    call ReadPhases(this%agsys_phases_inst)
+    call this%agsys_climate_inst%Init(bounds, this%agsys_phases_inst)
     call this%agsys_phenology_inst%Init(bounds)
 
   end subroutine Init

src/agsys/ctsm_interface/AgSysClimate.F90

@@ -9,6 +9,7 @@ module AgSysClimate
   use shr_kind_mod     , only : r8 => shr_kind_r8
   use shr_infnan_mod   , only : nan => shr_infnan_nan, assignment(=)
   use decompMod        , only : bounds_type
+  use AgSysPhases      , only : agsys_phases_type
   !
   implicit none
   private
@@ -19,8 +20,16 @@ module AgSysClimate
      private
 
      ! Public data members
-     real(r8), pointer, public :: accumulated_thermal_time_patch(:)        ! accumulated thermal time (deg-days)
-     real(r8), pointer, public :: accumulated_emerged_thermal_time_patch(:) ! accumulated thermal time since emergence (deg-days)
+     real(r8), pointer, public :: accumulated_thermal_time_patch(:)          ! accumulated thermal time (deg-days)
+
+     ! TODO(wjs, 2019-11-01) We may not need all of these - i.e., it maybe unnecessary to
+     ! have both an emerged_thermal_time and thermal time for each phase (since the former
+     ! can be calculated from the latter if needed). Also, we may not actually need the
+     ! full generality of having thermal time for each phase: it may be sufficient, for
+     ! example, to store the thermal time just for the previous phase. (If we can avoid
+     ! supporting this full generality, that could be good to avoid restart file bloat.)
+     real(r8), pointer, public :: accumulated_emerged_thermal_time_patch(:)  ! accumulated thermal time since emergence (deg-days)
+     real(r8), pointer, public :: accumulated_thermal_time_phases_patch(:,:) ! accumulated thermal time for each phase (deg-days) [phase, patch]
    contains
      procedure, public :: AgSysClimateTimeStep
 
@@ -61,32 +70,34 @@ end subroutine AgSysClimateTimeStep
   ! ========================================================================
 
   !-----------------------------------------------------------------------
-  subroutine Init(this, bounds)
+  subroutine Init(this, bounds, agsys_phases_inst)
     !
     ! !DESCRIPTION:
-    ! Initialize this agsys_climate_type insntance
+    ! Initialize this agsys_climate_type instance
     !
     ! !ARGUMENTS:
     class(agsys_climate_type), intent(inout) :: this
     type(bounds_type), intent(in) :: bounds
+    type(agsys_phases_type), intent(in) :: agsys_phases_inst
     !
     ! !LOCAL VARIABLES:
 
     character(len=*), parameter :: subname = 'Init'
     !-----------------------------------------------------------------------
 
-    call this%InitAllocate(bounds)
+    call this%InitAllocate(bounds, agsys_phases_inst)
   end subroutine Init
 
   !-----------------------------------------------------------------------
-  subroutine InitAllocate(this, bounds)
+  subroutine InitAllocate(this, bounds, agsys_phases_inst)
     !
     ! !DESCRIPTION:
     ! Allocate components of this agsys_climate_type instance
     !
     ! !ARGUMENTS:
     class(agsys_climate_type), intent(inout) :: this
     type(bounds_type), intent(in) :: bounds
+    type(agsys_phases_type), intent(in) :: agsys_phases_inst
     !
     ! !LOCAL VARIABLES:
 
@@ -101,6 +112,9 @@ subroutine InitAllocate(this, bounds)
     allocate(this%accumulated_thermal_time_patch(begp:endp))         ; this%accumulated_thermal_time_patch(:) = nan
     allocate(this%accumulated_emerged_thermal_time_patch(begp:endp)) ; this%accumulated_emerged_thermal_time_patch(:) = nan
 
+    allocate(this%accumulated_thermal_time_phases_patch(1:agsys_phases_inst%max_phases, begp:endp))
+    this%accumulated_thermal_time_phases_patch(:,:) = nan
+
     end associate
 
   end subroutine InitAllocate

src/agsys/ctsm_interface/AgSysParamReader.F90

@@ -9,12 +9,14 @@ module AgSysParamReader
   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
+  use AgSysPhases      , only : agsys_phases_type
   !
   implicit none
   private
 
   ! !PUBLIC ROUTINES:
   public :: ReadParams
+  public :: ReadPhases
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
@@ -37,4 +39,20 @@ subroutine ReadParams(params)
 
   end subroutine ReadParams
 
+  !-----------------------------------------------------------------------
+  subroutine ReadPhases(phases)
+    !
+    ! !DESCRIPTION:
+    ! Read phase descriptions for each crop
+    !
+    ! !ARGUMENTS:
+    type(agsys_phases_type), intent(inout) :: phases
+    !
+    ! !LOCAL VARIABLES:
+
+    character(len=*), parameter :: subname = 'ReadPhases'
+    !-----------------------------------------------------------------------
+
+  end subroutine ReadPhases
+
 end module AgSysParamReader

src/agsys/science/AgSysPhases.F90

@@ -0,0 +1,48 @@
+module AgSysPhases
+
+  !-----------------------------------------------------------------------
+  ! !DESCRIPTION:
+  ! Derived type describing the translation between a stage index and the phase / stage
+  ! names or phase type.
+  !
+  ! !USES:
+
+  !
+  implicit none
+  private
+
+  ! !PUBLIC DATA:
+
+  integer, parameter, public :: phase_type_unused = -1
+  integer, parameter, public :: phase_type_generic = 0
+  integer, parameter, public :: phase_type_germinating = 1
+  integer, parameter, public :: phase_type_emerging = 2
+  integer, parameter, public :: phase_type_node_number = 3
+  integer, parameter, public :: phase_type_leaf_appearance = 4
+  integer, parameter, public :: phase_type_end = 5
+  integer, parameter, public :: phase_type_maxval = 5
+
+  integer, parameter, public :: max_phase_name_len = 64  ! maximum number of characters in names of phases / stages
+
+  ! !PUBLIC TYPES:
+  type, public :: agsys_phases_type
+     private
+
+     ! Public data members
+     integer, public :: max_phases ! maximum number of phases used by any crop (arrays are dimensioned to be this large)
+     integer, allocatable, public :: num_phases_for_crop(:) ! [crop_type] number of phases used by each crop
+
+     ! Each of these arrays are dimensioned [stage, crop_type]. Stage is defined as a
+     ! point in time (e.g., the time of sowing, or the time of germination). Phase is
+     ! defined as the span of time between two stages (e.g., germinating is the phase
+     ! between sowing and germination). 'phase' variables give the phase whose start point
+     ! is the given stage. For example, if crop type 7 has the first two stages 'sowing'
+     ! and 'germination', then phase_name(1,7) = 'germinating'. Conversely, if
+     ! phase_name(3,7) = 'juvenile', then the name of the stage that triggers the start
+     ! of the juvenile phase is given by stage_name(3,7) (e.g., 'emergence').
+     character(len=max_phase_name_len), allocatable, public :: stage_name(:,:) ! [stage, crop_type]; name of the given stage
+     character(len=max_phase_name_len), allocatable, public :: phase_name(:,:) ! [stage, crop_type]; name of the phase whose start point is the given stage
+     integer                          , allocatable, public :: phase_type(:,:) ! [stage, crop_type]; each value is one of the above phase_type_* constants
+  end type agsys_phases_type
+
+end module AgSysPhases