Merge tag 'sci.1.80.3_api.37.0.0' into fatesluc_cbasedhrv_v2

Two-stream singularity correction update

This implements a more comprehensive avoidance of singularities with
two-stream radiation across bands.

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,29 +14,39 @@
 <!--- the model is expected to generated different answers -->
 <!--- from the master version of the code -->
 
-
-### Checklist:
+### Checklist
 <!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
-- [ ] My change requires a change to the documentation.
-- [ ] I have updated the in-code documentation .AND. (the [technical note](https://github.com/NGEET/fates-docs) .OR. the wiki) accordingly.
-- [ ] I have read the [**CONTRIBUTING**](https://github.com/NGEET/fates/blob/master/CONTRIBUTING.md) document.
+*If this is your first time contributing, please read the [**CONTRIBUTING**](https://github.com/NGEET/fates/blob/main/CONTRIBUTING.md) document.*
+
+All checklist items must be checked to enable merging this pull request:
+
+*Contributor*
+- [ ] The in-code documentation has been updated with descriptive comments
+- [ ] The documentation has been assessed to determine if updates are necessary
+
+*Integrator*
 - [ ] FATES PASS/FAIL regression tests were run
-- [ ] If answers were expected to change, evaluation was performed and provided
+- [ ] Evaluation of test results for answer changes was performed and results provided
 
+### Documentation
+<!--- If this pull requests warrants an update to the tech doc or user's guide, and said changes have been made paste a link to the documentation pull request below.  -->
+<!--- If documentation updates are needed, but changes do not yet have their own separate pull request, please create an issue on either repo so that we can keep track of necessary updates.-->
+- [Technical Note](https://github.com/NGEET/fates-docs) update:
+- [User's Guide](https://github.com/NGEET/fates-users-guide) update: 
 
 ### Test Results:
 <!--- Non-trivial changes require the PASS/FAIL regression tests. -->
 <!--- If changes to code are NOT expected to change answers, tests must -->
 <!--- be run against a baseline. -->
 
-CTSM (or) E3SM (specify which) test hash-tag:
+*CTSM (or) E3SM (specify which) test hash-tag:*
 
-CTSM (or) E3SM (specify which) baseline hash-tag:
+*CTSM (or) E3SM (specify which) baseline hash-tag:*
 
-FATES baseline hash-tag:
+*FATES baseline hash-tag:*
 
-Test Output:
+*Test Output:*
 
 <!--- paste in test results here -->
 

.gitignore

@@ -46,6 +46,10 @@ Thumbs.db
 *.dvi
 *.toc
 
+# Folders created with unit/functional tests
+_build/
+_run/
+
 
 # Old Files
 *~

.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

CMakeLists.txt

@@ -0,0 +1,90 @@
+cmake_minimum_required(VERSION 3.4)
+
+list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
+
+FIND_PATH(NETCDFC_FOUND libnetcdf.a ${NETCDF_C_DIR}/lib)
+FIND_PATH(NETCDFF_FOUND libnetcdff.a ${NETCDF_FORTRAN_DIR}/lib)
+MESSAGE(" NETCDFC_FOUND = ${NETCDFC_FOUND}")
+MESSAGE(" NETCDFF_FOUND = ${NETCDFF_FOUND}")
+
+string(APPEND LDFLAGS " -L${NETCDF_FORTRAN_DIR}/lib -lnetcdff")
+string(APPEND LDFLAGS " -L${NETCDF_C_DIR}/lib -lnetcdf")
+
+include(CIME_initial_setup)
+
+project(FATES_tests Fortran C)
+
+include(CIME_utils)
+
+set(HLM_ROOT "../../")
+
+# Add source directories from other share code (csm_share, etc.)
+add_subdirectory(${HLM_ROOT}/share/src csm_share)
+add_subdirectory(${HLM_ROOT}/share/unit_test_stubs/util csm_share_stubs)
+
+# Add FATES source directories
+add_subdirectory(${HLM_ROOT}/src/fates/main fates_main)
+add_subdirectory(${HLM_ROOT}/src/fates/biogeochem fates_biogeochem)
+add_subdirectory(${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(${HLM_ROOT}/src/fates/radiation fates_radiation)
+add_subdirectory(${HLM_ROOT}/src/fates/testing/testing_shr test_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
+#
+# TODO: 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_mpi_mod.F90")
+foreach (sourcefile ${share_sources})
+  string(REGEX MATCH "shr_mpi_mod.F90" match_found ${sourcefile})
+  if(match_found)
+    list(REMOVE_ITEM share_sources ${sourcefile})
+  endif()
+endforeach()
+
+# Remove shr_cal_mod from share_sources.
+#
+# shr_cal_mod depends on ESMF (or the lightweight esmf wrf timemgr, at
+# least). Since CTSM doesn't currently use shr_cal_mod, we're avoiding
+# the extra overhead of including esmf_wrf_timemgr sources in this
+# build.
+#
+# TODO: like above, this should be moved into a general-purpose function
+# in Sourcelist_utils.  Then this block of code could be replaced with a
+# single call, like: remove_source_file(${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()
+
+# 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 ${share_sources})
+declare_generated_dependencies(csm_share "${share_genf90_sources}")
+add_library(fates ${fates_sources})
+add_dependencies(fates csm_share)
+
+# We need to look for header files here, in order to pick up shr_assert.h
+include_directories(${HLM_ROOT}/share/include)
+
+# This needs to be something we add dynamically
+# via some calls using cime
+set(NETCDF_C_DIR ${NETCDF_C_PATH})
+set(NETCDF_FORTRAN_DIR ${NETCDF_F_PATH})
+
+include_directories(${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(${CMAKE_CURRENT_BINARY_DIR})
+
+# Add the main test directory
+add_subdirectory(${HLM_ROOT}/src/fates/testing)

biogeochem/CMakeLists.txt

@@ -0,0 +1,9 @@
+# This file is required for unit testing, but is not used for production runs
+list(APPEND fates_sources
+  FatesLitterMod.F90
+  FatesCohortMod.F90
+  FatesAllometryMod.F90
+  DamageMainMod.F90
+  FatesPatchMod.F90)
+
+sourcelist_to_parent(fates_sources)

biogeochem/DamageMainMod.F90

@@ -11,10 +11,6 @@ module DamageMainMod
   use EDPftvarcon           , only : EDPftvarcon_inst
   use EDParamsMod           , only : damage_event_code
   use EDParamsMod           , only : ED_val_history_damage_bin_edges
-  use EDTypesMod            , only : ed_site_type
-  use EDTypesMod            , only : ed_patch_type
-  use EDTypesMod            , only : ed_cohort_type
-  use EDTypesMod            , only : AREA
   use FatesInterfaceTypesMod, only : hlm_current_day
   use FatesInterfaceTypesMod, only : hlm_current_month
   use FatesInterfaceTypesMod, only : hlm_current_year
@@ -54,7 +50,7 @@ module DamageMainMod
 
 
 
-  subroutine IsItDamageTime(is_master, currentSite)
+  subroutine IsItDamageTime(is_master)
 
     !----------------------------------------------------------------------------
     ! This subroutine determines whether damage should occur (it is called daily)
@@ -63,7 +59,7 @@ subroutine IsItDamageTime(is_master, currentSite)
 
 
     integer, intent(in) :: is_master
-    type(ed_site_type), intent(inout), target :: currentSite
+    !type(ed_site_type), intent(inout), target :: currentSite
 
     integer :: icode     ! Integer equivalent of the event code (parameter file only allows reals)
     integer :: damage_date  ! Day of month for damage extracted from event code