Merge tag 'sci.1.81.1_api.37.1.0' into parameter-switch-migration

An alternative method of conserving patch area for two-stream radiation.
NGEET · Feb 20, 2025 · 2a6b33e · 2a6b33e
2 parents 9cb1611 + 655d784
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diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml
@@ -0,0 +1,71 @@
+name: Bug Report
+description: Issues related to the model crashing or the other unexpected behavior
+# title: "[Bug]: "
+# labels: ["bug - science"]
+# projects: ["octo-org/1", "octo-org/44"]
+# assignees:
+  # - octocat
+body:
+  - type: markdown
+    attributes:
+      value: "Please describe the issue below"
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the issue
+      description: Provide detail on the expected behavior and observed behavior.  Attached screen shots and plots as necessary.
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: shell
+  - type: input
+    id: fates-tag
+    attributes:
+      label: FATES tag
+      description: The output from running `git describe` in the fates directory
+      placeholder: e.g. sci.1.80.11_api.37.0.0
+    validations:
+      required: true
+  - type: input
+    id: hlm-tag
+    attributes:
+      label: Host land model tag
+      description: The output from running `git describe` in the host land model directory
+      placeholder: e.g. ctsm5.3.022
+    validations:
+      required: true
+  - type: dropdown
+    id: machine
+    attributes:
+      label: Machine
+      options:
+        - perlmutter
+        - derecho
+        - izumi
+        - other HLM supported machine
+        - personal computer
+    validations:
+      required: true
+  - type: input
+    id: other-machine
+    attributes:
+      label: Other supported machine name
+      placeholder: e.g. frontier
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Please provide any additional context that you think is relevant such as your personal computer environment if applicable.
+      placeholder: e.g. Ubuntu 22.04
+  # - type: checkboxes
+  #   id: terms
+  #   attributes:
+  #     label: Code of Conduct
+  #     description: By submitting this issue, you agree to follow our [Code of Conduct](https://example.com).
+  #     options:
+  #       - label: I agree to follow this project's Code of Conduct
+  #         required: true
diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml
@@ -0,0 +1,30 @@
+name: Feature request
+description: Suggest a new feature or update to an existing feature
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: "Please describe your feature suggestion below.  Also consider opening a [discussion board thread](https://github.com/NGEET/fates/discussions/categories/ideas) for broader ideas."
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the changes
+      description: A clear and concise description of what you want to happen
+    validations:
+      required: true
+  - type: textarea
+    id: problem
+    attributes:
+      label: Is your request related to a problem?
+      description: A short description of the impetus for the request, if any.
+      placeholder: e.g. This parameter should be indexed by pft, not globally [...]
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternative options
+      description: Describe alternatives to be considered as necessary
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Provide additional context including attachements or references, as necessary
diff --git a/.github/ISSUE_TEMPLATE/task.yml b/.github/ISSUE_TEMPLATE/task.yml
@@ -0,0 +1,14 @@
+name: Task
+description: General issue that describes a specific task to be completed.
+body:
+  - type: markdown
+    attributes:
+      value: "Describe the task below."
+  - type: textarea
+    id: description
+    attributes:
+      label: Task description
+      description: Provide detail about the necessary task with sub-steps if applicable.
+      placeholder: e.g. update the refactor the patch fusion subroutine
+    validations:
+      required: true
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,7 @@
 cmake_minimum_required(VERSION 3.4)
 
 list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../share/cmake")
 
 FIND_PATH(NETCDFC_FOUND libnetcdf.a ${NETCDF_C_DIR}/lib)
 FIND_PATH(NETCDFF_FOUND libnetcdff.a ${NETCDF_FORTRAN_DIR}/lib)
@@ -29,7 +30,10 @@ add_subdirectory(${HLM_ROOT}/src/fates/biogeophys fates_biogeophys)
 add_subdirectory(${HLM_ROOT}/src/fates/parteh fates_parteh)
 add_subdirectory(${HLM_ROOT}/src/fates/fire fates_fire)
 add_subdirectory(${HLM_ROOT}/src/fates/radiation fates_radiation)
+
+# Testing directories
 add_subdirectory(${HLM_ROOT}/src/fates/testing/testing_shr test_share)
+add_subdirectory(${HLM_ROOT}/src/fates/testing/functional_testing/fire/shr fire_share)
 
 # Remove shr_mpi_mod from share_sources.
 # This is needed because we want to use the mock shr_mpi_mod in place of the real one
@@ -45,23 +49,21 @@ foreach (sourcefile ${share_sources})
 endforeach()
 
 # Remove shr_cal_mod from share_sources.
-#
-# shr_cal_mod depends on ESMF (or the lightweight esmf wrf timemgr, at
-# least). Since CTSM doesn't currently use shr_cal_mod, we're avoiding
-# the extra overhead of including esmf_wrf_timemgr sources in this
-# build.
-#
-# TODO: like above, this should be moved into a general-purpose function
-# in Sourcelist_utils.  Then this block of code could be replaced with a
-# single call, like: remove_source_file(${share_sources}
-# "shr_cal_mod.F90")
 foreach (sourcefile ${share_sources})
   string(REGEX MATCH "shr_cal_mod.F90" match_found ${sourcefile})
   if(match_found)
     list(REMOVE_ITEM share_sources ${sourcefile})
   endif()
 endforeach()
 
+# Remove shr_pio_mod from share_sources.
+foreach (sourcefile ${share_sources})
+  string(REGEX MATCH "shr_pio_mod.F90" match_found ${sourcefile})
+  if(match_found)
+    list(REMOVE_ITEM share_sources ${sourcefile})
+  endif()
+endforeach()
+
 # Build libraries containing stuff needed for the unit tests.
 # Eventually, these add_library calls should probably be distributed into the correct location, rather than being in this top-level CMakeLists.txt file.
 add_library(csm_share ${share_sources})
@@ -81,10 +83,13 @@ include_directories(${NETCDF_C_DIR}/include
                     ${NETCDF_FORTRAN_DIR}/include)
 link_directories(${NETCDF_C_DIR}/lib
                 ${NETCDF_FORTRAN_DIR}/lib)
+
 
 # Tell cmake to look for libraries & mod files here, because this is where we built libraries
 include_directories(${CMAKE_CURRENT_BINARY_DIR})
-link_directories(${CMAKE_CURRENT_BINARY_DIR})
 
+# Directories and libraries to include in the link step
+link_directories(${CMAKE_CURRENT_BINARY_DIR})
+
 # Add the main test directory
 add_subdirectory(${HLM_ROOT}/src/fates/testing)
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -29,7 +29,7 @@ We aim to create an open development environment for FATES where scientists can
 * Document the version of the code used in any publication, preferably by  using a release tag (existing or newly created) if possible, or a commit hash if not.
 * Do not use code from anywhere other than the central FATES development repository (the “master” branch of the “NGEET/fates“ github repository) without discussing with the author(s) of the modified code your intentions for using the code and receiving their permission to do so.
 * When using model features that have recently been integrated into the central FATES development repository, be mindful of the contributions of others and, where the novel features qualitatively affect the results of a given simulation, involve the author(s) of these features in any resulting manuscripts.  Be particularly aware of the concerns of early career researchers, and ensure they have sufficient opportunities to lead publications using their developments.
-* When discussing results arising from older model features that have been described in the literature, accurately cite the publications describing those features or releases. A list of some relevant publications can be found at [https://github.com/NGEET/fates/wiki/Relevant-References][wiki_ref_page]
+* When discussing results arising from older model features that have been described in the literature, accurately cite the publications describing those features or releases. A list of some relevant publications can be found in the [users guide](https://fates-users-guide.readthedocs.io/en/latest/user/Reference-List.html).
 
 ## Our Responsibilities
 

diff --git a/biogeochem/CMakeLists.txt b/biogeochem/CMakeLists.txt
@@ -4,6 +4,7 @@ list(APPEND fates_sources
   FatesCohortMod.F90
   FatesAllometryMod.F90
   DamageMainMod.F90
+  EDCohortDynamicsMod.F90
   FatesPatchMod.F90)
 
 sourcelist_to_parent(fates_sources)
diff --git a/biogeochem/EDCanopyStructureMod.F90 b/biogeochem/EDCanopyStructureMod.F90
@@ -18,9 +18,9 @@ module EDCanopyStructureMod
   use FatesAllometryMod     , only : carea_allom
   use EDCohortDynamicsMod   , only : terminate_cohorts, terminate_cohort, fuse_cohorts
   use EDCohortDynamicsMod   , only : InitPRTObject
-  use FatesAllometryMod     , only : tree_lai
-  use FatesAllometryMod     , only : tree_sai
+  use FatesAllometryMod     , only : tree_lai_sai
   use EDTypesMod            , only : ed_site_type
+  use EDTypesMod            , only : set_patchno
   use FatesAllometryMod     , only : VegAreaLayer
   use FatesAllometryMod     , only : CrownDepth
   use FatesPatchMod,          only : fates_patch_type
@@ -1313,8 +1313,6 @@ subroutine canopy_summarization( nsites, sites, bc_in )
     ! ---------------------------------------------------------------------------------
 
     use FatesInterfaceTypesMod    , only : hlm_use_cohort_age_tracking
-    use FatesInterfaceTypesMod    , only : hlm_radiation_model
-    use EDPatchDynamicsMod        , only : set_patchno
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
     use EDtypesMod                , only : area
@@ -1351,7 +1349,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )
        ! driving model.  Loops through all patches and sets cpatch%patchno to the integer
        ! order of oldest to youngest where the oldest is 1.
        ! --------------------------------------------------------------------------------
-       call set_patchno( sites(s) )
+       call set_patchno( sites(s) , .false., 0)
 
        currentPatch => sites(s)%oldest_patch
 
@@ -1897,7 +1895,6 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
 
     do s = 1,nsites
 
-       ifp = 0
        total_patch_area = 0._r8
        total_canopy_area = 0._r8
        bc_out(s)%canopy_fraction_pa(:) = 0._r8
@@ -1909,9 +1906,8 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
        c = fcolumn(s)
        do while(associated(currentPatch))
 
-          if(currentPatch%nocomp_pft_label.ne.nocomp_bareground)then  ! ignore the bare-ground-PFT patch entirely for these BC outs
-
-             ifp = ifp+1
+          ifp = currentPatch%patchno
+          if_bare: if(currentPatch%nocomp_pft_label.ne.nocomp_bareground)then  ! ignore the bare-ground-PFT patch entirely for these BC outs
 
              if ( currentPatch%total_canopy_area-currentPatch%area > 0.000001_r8 ) then
                 if(debug)then
@@ -2029,7 +2025,7 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
 
              total_patch_area = total_patch_area + currentPatch%area/AREA
 
-          end if
+          end if if_bare
           currentPatch => currentPatch%younger
        end do
 
@@ -2049,13 +2045,11 @@ subroutine update_hlm_dynamics(nsites,sites,fcolumn,bc_out)
           end if
 
           currentPatch => sites(s)%oldest_patch
-          ifp = 0
           do while(associated(currentPatch))
+             ifp = currentPatch%patchno
              if(currentPatch%nocomp_pft_label.ne.nocomp_bareground)then ! for vegetated patches only
-                ifp = ifp+1
                 bc_out(s)%canopy_fraction_pa(ifp) = bc_out(s)%canopy_fraction_pa(ifp)/total_patch_area
              endif ! veg patch
-
              currentPatch => currentPatch%younger
           end do
 
@@ -2245,7 +2239,7 @@ subroutine UpdateCohortLAI(currentCohort, canopy_layer_tlai, total_canopy_area)
    ! Update LAI and related variables for a given cohort
 
    ! Uses
-   use EDParamsMod, only : dlower_vai
+   use EDParamsMod, only : dlower_vai, dinc_vai
 
    ! Arguments
    type(fates_cohort_type),intent(inout), target   :: currentCohort
@@ -2254,26 +2248,30 @@ subroutine UpdateCohortLAI(currentCohort, canopy_layer_tlai, total_canopy_area)
 
    ! Local variables
    real(r8) :: leaf_c                              ! leaf carbon [kg]
-
+   real(r8) :: treesai                             ! stem area index within crown m2/m2
+
    ! Obtain the leaf carbon
    leaf_c = currentCohort%prt%GetState(leaf_organ,carbon12_element)
 
-
-   ! Note that tree_lai has an internal check on the canopy locatoin
-   currentCohort%treelai = tree_lai(leaf_c, currentCohort%pft, currentCohort%c_area, &
-        currentCohort%n, currentCohort%canopy_layer,               &
-        canopy_layer_tlai,currentCohort%vcmax25top )
-
+   ! Note that tree_lai has an internal check on the canopy location
+   call  tree_lai_sai(leaf_c, currentCohort%pft, currentCohort%c_area, currentCohort%n,           &
+          currentCohort%canopy_layer, canopy_layer_tlai, currentCohort%vcmax25top, currentCohort%dbh, currentCohort%crowndamage,          &
+          currentCohort%canopy_trim, currentCohort%efstem_coh, 4, currentCohort%treelai, treesai )
+
+   ! Do not update stem area index of SP vegetation
    if (hlm_use_sp .eq. ifalse) then
-      currentCohort%treesai = tree_sai(currentCohort%pft, currentCohort%dbh, currentCohort%crowndamage, &
-                                       currentCohort%canopy_trim, currentCohort%efstem_coh, &
-                                       currentCohort%c_area, currentCohort%n, currentCohort%canopy_layer, &
-                                       canopy_layer_tlai, currentCohort%treelai , &
-                                       currentCohort%vcmax25top,4)
+      currentCohort%treesai = treesai
    end if
-
+   
    ! Number of actual vegetation layers in this cohort's crown
    currentCohort%nv =  count((currentCohort%treelai+currentCohort%treesai) .gt. dlower_vai(:)) + 1
+
+   if( currentCohort%nv .ne. minloc(dlower_vai, DIM=1, MASK=(dlower_vai>(currentCohort%treelai+currentCohort%treesai))) ) then
+      write(fates_log(),*) 'We use two methods of finding maximum leaf layers, and they are not equivalent'
+      write(fates_log(),*) 'count method:',currentCohort%nv
+      write(fates_log(),*) 'minloc method:',minloc(dlower_vai, DIM=1, MASK=(dlower_vai>(currentCohort%treelai+currentCohort%treesai)))
+      call endrun(msg=errMsg(sourcefile, __LINE__))
+   end if
 
   end subroutine UpdateCohortLAI