Merge tag 'sci.1.80.6_api.37.0.0' into grazing_merge

Bug fix for issue #1301 Corrects when the fraction of burnt fuel is zero'd and how the litter mass is updated based on that fraction.
NGEET · Jan 13, 2025 · b3113b7 · b3113b7
2 parents ac5bf38 + 1689466
commit b3113b7
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Showing 90 changed files with 8,782 additions and 3,128 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,13 @@
+# This is a git submodule file to include additional submodules when FATES is checkout out.
+#
+# It includes optional additional support for
+# git-fleximod (https://github.com/ESMCI/git-fleximod)
+# that will be used when git-fleximod is used to check it out (i.e. for CESM)
+#
+[submodule "tools/landusedata"]
+	path = tools/landusedata
+	url = https://github.com/NGEET/tools-fates-landusedata
+	fxtag = v0.1.1
+	fxrequired = AlwaysRequired
+	# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+	fxDONOTUSEurl = https://github.com/NGEET/tools-fates-landusedata
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/biogeochem/EDCanopyStructureMod.F90 b/biogeochem/EDCanopyStructureMod.F90
diff --git a/biogeochem/EDCohortDynamicsMod.F90 b/biogeochem/EDCohortDynamicsMod.F90
@@ -45,6 +45,7 @@ Module EDCohortDynamicsMod
   use PRTGenericMod         , only : max_nleafage
   use FatesConstantsMod     , only : ican_upper
   use EDTypesMod            , only : site_fluxdiags_type
+  use EDTypesMod            , only : elem_diag_type
   use PRTGenericMod         , only : num_elements
   use FatesConstantsMod     , only : leaves_on
   use FatesConstantsMod     , only : leaves_off
@@ -602,7 +603,7 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant,bc_in)
     type(bc_in_type), intent(in)    :: bc_in
 
     type(litter_type), pointer        :: litt       ! Litter object for each element
-    type(site_fluxdiags_type),pointer :: flux_diags
+    type(elem_diag_type),pointer :: elflux_diags
 
     real(r8) :: leaf_m    ! leaf mass [kg]
     real(r8) :: store_m   ! storage mass [kg]
@@ -646,7 +647,7 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant,bc_in)
        endif
 
        litt => cpatch%litter(el)
-       flux_diags => csite%flux_diags(el)
+       elflux_diags => csite%flux_diags%elem(el)
 
        !adjust how wood is partitioned between the cwd classes based on cohort dbh
        call adjust_SF_CWD_frac(ccohort%dbh,ncwd,SF_val_CWD_frac,SF_val_CWD_frac_adj)
@@ -667,12 +668,12 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant,bc_in)
           enddo
 
           ! above ground
-          flux_diags%cwd_ag_input(c)  = flux_diags%cwd_ag_input(c) + &
+          elflux_diags%cwd_ag_input(c)  = elflux_diags%cwd_ag_input(c) + &
                 (struct_m+sapw_m) * SF_val_CWD_frac_adj(c) * &
                 prt_params%allom_agb_frac(pft) * nplant
 
           ! below ground
-          flux_diags%cwd_bg_input(c)  = flux_diags%cwd_bg_input(c) + &
+          elflux_diags%cwd_bg_input(c)  = elflux_diags%cwd_bg_input(c) + &
                 (struct_m + sapw_m) * SF_val_CWD_frac_adj(c) * &
                 (1.0_r8 - prt_params%allom_agb_frac(pft)) * nplant
 
@@ -692,11 +693,11 @@ subroutine SendCohortToLitter(csite,cpatch,ccohort,nplant,bc_in)
 
        end do
 
-       flux_diags%leaf_litter_input(pft) = &
-             flux_diags%leaf_litter_input(pft) +  &
+       elflux_diags%surf_fine_litter_input(pft) = &
+             elflux_diags%surf_fine_litter_input(pft) +  &
              (leaf_m+repro_m) * nplant
-       flux_diags%root_litter_input(pft) = &
-             flux_diags%root_litter_input(pft) +  &
+       elflux_diags%root_litter_input(pft) = &
+             elflux_diags%root_litter_input(pft) +  &
              (fnrt_m+store_m) * nplant
 
 
@@ -1066,20 +1067,24 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
                                            nextc%n*nextc%gpp_acc)/newn
                                       currentCohort%npp_acc        = (currentCohort%n*currentCohort%npp_acc     + &
                                            nextc%n*nextc%npp_acc)/newn
-                                      currentCohort%resp_acc       = (currentCohort%n*currentCohort%resp_acc    + &
-                                           nextc%n*nextc%resp_acc)/newn
-                                      currentCohort%resp_acc_hold  = &
-                                           (currentCohort%n*currentCohort%resp_acc_hold + &
-                                           nextc%n*nextc%resp_acc_hold)/newn
+                                      currentCohort%resp_m_acc       = (currentCohort%n*currentCohort%resp_m_acc    + &
+                                           nextc%n*nextc%resp_m_acc)/newn
+                                      currentCohort%resp_m_acc_hold  = &
+                                           (currentCohort%n*currentCohort%resp_m_acc_hold + &
+                                           nextc%n*nextc%resp_m_acc_hold)/newn
+                                      currentCohort%resp_g_acc_hold  = &
+                                           (currentCohort%n*currentCohort%resp_g_acc_hold + &
+                                           nextc%n*nextc%resp_g_acc_hold)/newn
                                       currentCohort%npp_acc_hold   = &
                                            (currentCohort%n*currentCohort%npp_acc_hold + &
                                            nextc%n*nextc%npp_acc_hold)/newn
                                       currentCohort%gpp_acc_hold   = &
                                            (currentCohort%n*currentCohort%gpp_acc_hold + &
                                            nextc%n*nextc%gpp_acc_hold)/newn
 
-                                      currentCohort%resp_excess = (currentCohort%n*currentCohort%resp_excess + &
-                                           nextc%n*nextc%resp_excess)/newn
+                                      currentCohort%resp_excess_hold = &
+                                           (currentCohort%n*currentCohort%resp_excess_hold + &
+                                           nextc%n*nextc%resp_excess_hold)/newn
 
                                       currentCohort%dmort          = (currentCohort%n*currentCohort%dmort       + &
                                            nextc%n*nextc%dmort)/newn