Merge pull request #1 from rgknox/xlg-grass-allometry-rgk

remove damage and parameter changes, merge in main

.gitignore

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

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/EDMortalityFunctionsMod.F90

@@ -281,7 +281,7 @@ end subroutine mortality_rates
 
  subroutine Mortality_Derivative( currentSite, currentCohort, bc_in, btran_ft, &
       mean_temp, land_use_label, age_since_anthro_disturbance,       &
-      frac_site_primary, harvestable_forest_c, harvest_tag)
+      frac_site_primary, frac_site_secondary, harvestable_forest_c, harvest_tag)
 
     !
     ! !DESCRIPTION:
@@ -301,6 +301,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in, btran_ft, &
     integer,          intent(in)               :: land_use_label
     real(r8),         intent(in)               :: age_since_anthro_disturbance
     real(r8),         intent(in)               :: frac_site_primary
+    real(r8),         intent(in)               :: frac_site_secondary
 
     real(r8), intent(in) :: harvestable_forest_c(:)   ! total carbon available for logging, kgC site-1
     integer, intent(out) :: harvest_tag(:)    ! tag to record the harvest status
@@ -329,7 +330,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in, btran_ft, &
     !if trees are in the canopy, then their death is 'disturbance'. This probably needs a different terminology
     call mortality_rates(currentCohort,bc_in,btran_ft, mean_temp,              &
       cmort,hmort,bmort,frmort, smort, asmort, dgmort)
-    call LoggingMortality_frac(ipft, currentCohort%dbh, currentCohort%canopy_layer, &
+    call LoggingMortality_frac(currentSite, bc_in, ipft, currentCohort%dbh, currentCohort%canopy_layer, &
                                currentCohort%lmort_direct,                       &
                                currentCohort%lmort_collateral,                    &
                                currentCohort%lmort_infra,                        &
@@ -339,7 +340,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in, btran_ft, &
                                bc_in%hlm_harvest_units, &
                                land_use_label, &
                                age_since_anthro_disturbance, &
-                               frac_site_primary, harvestable_forest_c, harvest_tag)
+                               frac_site_primary, frac_site_secondary, harvestable_forest_c, harvest_tag)
 
     if (currentCohort%canopy_layer > 1)then 
        ! Include understory logging mortality rates not associated with disturbance