Fix some bugs in testing

CMakeLists.txt

@@ -2,6 +2,7 @@ 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")
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../components/cmeps/cmake")
 
 FIND_PATH(NETCDFC_FOUND libnetcdf.a ${NETCDF_C_DIR}/lib)
 FIND_PATH(NETCDFF_FOUND libnetcdff.a ${NETCDF_FORTRAN_DIR}/lib)
@@ -19,6 +20,23 @@ include(CIME_utils)
 
 set(HLM_ROOT "../../")
 
+if (DEFINED ENV{ESMF_ROOT})
+  list(APPEND CMAKE_MODULE_PATH $ENV{ESMF_ROOT}/cmake)
+endif()
+find_package(ESMF REQUIRED)
+
+# This adds include directories needed for ESMF
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${ESMF_F90COMPILEPATHS} ")
+# This (which is *not* done in the share CMakeLists.txt) adds all directories and
+# libraries needed when linking ESMF, including any dependencies of ESMF. (But note that
+# this does *not* include the "-lesmf" itself). In particular, note that this includes any
+# link flags needed to link against PIO, which is needed on some systems (including
+# derecho); bringing in these PIO-related link flags via this ESMF mechanism allows us to
+# avoid explicitly including PIO as a link library, which wouldn't work on systems where
+# there is no separate PIO library and instead ESMF is built with its internal PIO
+# library.
+link_libraries(${ESMF_INTERFACE_LINK_LIBRARIES})
+
 # 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)
@@ -90,6 +108,7 @@ include_directories(${CMAKE_CURRENT_BINARY_DIR})
 
 # Directories and libraries to include in the link step
 link_directories(${CMAKE_CURRENT_BINARY_DIR})
+link_libraries(esmf)
 
 # Add the main test directory
 add_subdirectory(${HLM_ROOT}/src/fates/testing)

biogeophys/CMakeLists.txt

@@ -1,5 +1,6 @@
 list(APPEND fates_sources
   FatesHydroWTFMod.F90
+  LeafBiophysicsMod.F90
   FatesPlantHydraulicsMod.F90)
 
 sourcelist_to_parent(fates_sources)

testing/cime_setup.md

@@ -72,9 +72,6 @@ Next set up some other environment variables:
 
 ```bash
 export ESMF_INSTALL_PREFIX=$ESMF_DIR/install_dir
-export ESMF_NETCDF=split
-export ESMF_NETCDF_INCLUDE=/usr/local/include
-export ESMF_NETCDF_LIBPATH=/usr/local/lib
 export ESMF_COMM=openmpi
 export ESMF_COMPILER=gfortranclang
 ```

testing/functional_testing/math_utils/FatesTestMathUtils.F90

@@ -1,7 +1,7 @@
 program FatesTestQuadSolvers
 
   use FatesConstantsMod, only : r8 => fates_r8
-  use FatesUtilsMod,     only : QuadraticRootsNSWC, QuadraticRootsSridharachary
+  use FatesUtilsMod,     only : QuadraticRootsNSWC
   use FatesUtilsMod,     only : GetNeighborDistance
 
   implicit none
@@ -15,6 +15,7 @@ program FatesTestQuadSolvers
   real(r8) :: a(n), b(n), c(n) ! coefficients for quadratic solvers
   real(r8) :: root1(n)         ! real part of first root of quadratic solver
   real(r8) :: root2(n)         ! real part of second root of quadratic solver
+  logical  :: err              ! error
 
   interface
 
@@ -42,7 +43,7 @@ end subroutine WriteQuadData
   c = (/1.0_r8, 12.0_r8, 3.0_r8, 1.1_r8/)
 
   do i = 1, n
-    call QuadraticRootsNSWC(a(i), b(i), c(i), root1(i), root2(i))
+    call QuadraticRootsNSWC(a(i), b(i), c(i), root1(i), root2(i), err)
   end do
 
   call WriteQuadData(out_file, n, a, b, c, root1, root2)

testing/testing_shr/FatesFactoryMod.F90

@@ -8,6 +8,7 @@ module FatesFactoryMod
   use FatesConstantsMod,           only : isemi_stress_decid
   use FatesConstantsMod,           only : primaryland
   use FatesConstantsMod,           only : sec_per_day, days_per_year
+  use FatesConstantsMod,           only : default_regeneration
   use FatesGlobals,                only : fates_log
   use FatesGlobals,                only : endrun => fates_endrun
   use FatesCohortMod,              only : fates_cohort_type
@@ -53,10 +54,9 @@ module FatesFactoryMod
   use FatesAllometryMod,           only : bdead_allom
   use FatesAllometryMod,           only : bstore_allom
   use FatesAllometryMod,           only : carea_allom
-  use FatesInterfaceTypesMod,      only : hlm_parteh_mode
+  use FatesInterfaceTypesMod,      only : hlm_parteh_mode, hlm_regeneration_model
   use FatesInterfaceTypesMod,      only : nleafage
   use FatesSizeAgeTypeIndicesMod,  only : get_age_class_index
-  use EDParamsMod,                 only : regeneration_model
   use SyntheticPatchTypes,         only : synthetic_patch_type
   use shr_log_mod,                 only : errMsg => shr_log_errMsg
 
@@ -89,6 +89,8 @@ subroutine InitializeGlobals(step_size)
     element_pos(carbon12_element) = 1
     call InitPRTGlobalAllometricCarbon()
 
+    hlm_regeneration_model = default_regeneration
+
     allocate(ema_24hr)
     call ema_24hr%define(sec_per_day, step_size, moving_ema_window)
     allocate(fixed_24hr)
@@ -445,7 +447,7 @@ subroutine PatchFactory(patch, age, area, num_swb, num_pft, num_levsoil,
 
     allocate(patch)
     call patch%Create(age, area, land_use_label_local, nocomp_pft_local, num_swb,        &
-      num_pft, num_levsoil, tod_local, regeneration_model)
+      num_pft, num_levsoil, tod_local, default_regeneration)
 
     patch%patchno = 1
     patch%younger => null()