Merge branch 'steveghan/atm/iediagnostics' (PR #1400)

Add aerosol and cloud history for diagnosing aerosol effects on cloud...

radiative forcing

Add aerosol and cloud history for diagnosing relationships that drive
aerosol effects on cloud radiative forcing. The additional fields are
calculated if namelist option do_aerocom_ind3 =.true. and written
every 3 hours if atm_in contains:
mfilt          = 1,8
nhtfrq         = 0,-3
fincl2 = 'AODVIS:A', 'angstrm:A','cod:A', 'cdr:A', 'cdnc:A', 'cdnum:A',
'icnum:A',  'clt:A', 'lcc:A', 'lwp:A', 'iwp:A', 'icc:A', 'icnc:A',
'icr:A', 'LHFLX:A', 'SHFLX:A', 'OMEGA500:A', 'rh700:A', 'colrv:A',
'ccn:A', 'ccn.1bl:A', 'ccn.3bl:A', 'ptop:A', 'ttop:A', 'rwp:A','lwp2:A',
'iwp2:A', 'autoconv:A','accretn:A', 'FSUTOA_d1:A', 'FSUTOAC_d1:A',
'FSUTOA:A', 'FSUTOAC:A', 'FLUT:A', 'FLUTC:A','TH7001000', 'PRECL:A'
rad_diag_1             = 'A:Q:H2O', 'N:O2:O2', 'N:CO2:CO2', 'A:O3:O3',
'N:N2O:N2O', 'N:CH4:CH4', 'N:CFC11:CFC11', 'N:CFC12:CFC12'

[BFB]
[NML]

* steveghan/atm/iediagnostics:
  Modified "use abortutils" to "use cam_abortutils"
  mods to set do_aerocom_ind3 with namelist - Steve Ghan 4-11-2017
  aerosol indirect effects diagnostics mods - Steve Ghan 4-11-2017
  aerosol indirect effects diagnostics - Steve Ghan 4-11-2017

Conflicts:
	components/cam/src/physics/cam/phys_control.F90

CMakeLists.txt

@@ -2,13 +2,15 @@ cmake_minimum_required(VERSION 2.8)
 include(ExternalProject)
 set(CIME_ROOT "${CMAKE_CURRENT_SOURCE_DIR}")
 
+list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
+include(CIME_initial_setup)
+
 project(cime_tests Fortran C)
 
 # We rely on pio for cmake utilities like findnetcdf.cmake, so that we don't
 # need to duplicate this cmake code
-list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/externals/pio2/cmake")
+list(APPEND CMAKE_MODULE_PATH "${CIME_ROOT}/src/externals/pio2/cmake")
 
-list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
 include(CIME_utils)
 find_package(NetCDF COMPONENTS C Fortran)
 include_directories(${NetCDF_C_INCLUDE_DIRS} ${NetCDF_Fortran_INCLUDE_DIRS})
@@ -19,16 +21,23 @@ include_directories(${NetCDF_C_INCLUDE_DIRS} ${NetCDF_Fortran_INCLUDE_DIRS})
 # ------------------------------------------------------------------------
 # Build mct
 # ------------------------------------------------------------------------
-set(MCT_ROOT "${CIME_ROOT}/externals/mct")
+set(MCT_ROOT "${CIME_ROOT}/src/externals/mct")
+
+if (USE_MPI_SERIAL)
+  set(ENABLE_MPI_SERIAL "--enable-mpiserial")
+else()
+  set(ENABLE_MPI_SERIAL "")
+endif()
 
 ExternalProject_add(mct_project
   PREFIX ${CMAKE_CURRENT_BINARY_DIR}
   SOURCE_DIR ${MCT_ROOT}
   BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/mct
-  CONFIGURE_COMMAND ${MCT_ROOT}/configure --enable-debugging --prefix=${CMAKE_CURRENT_BINARY_DIR} CFLAGS=${CFLAGS} FCFLAGS=${FFLAGS} SRCDIR=${MCT_ROOT} DEBUG="-g"
-  BUILD_COMMAND $(MAKE)
+  CONFIGURE_COMMAND ${MCT_ROOT}/configure ${ENABLE_MPI_SERIAL} --enable-debugging --prefix=${CMAKE_CURRENT_BINARY_DIR} CC=${CMAKE_C_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=${CFLAGS} FCFLAGS=${FFLAGS} SRCDIR=${MCT_ROOT} DEBUG="-g"
+  BUILD_COMMAND $(MAKE) SRCDIR=${MCT_ROOT}
   # Leave things in <BINARY_DIR> rather than "installing", because we have
-  # no need to move things around inside of the CMake binary directory.
+  # no need to move things around inside of the CMake binary directory. Also,
+  # mpi-serial doesn't install properly in the out-of-source build
   INSTALL_COMMAND :
   )
 # This copy_makefiles step is needed because mct currently doesn't support an
@@ -43,12 +52,27 @@ ExternalProject_add_step(mct_project copy_makefiles
   COMMAND mkdir -p mpeu
   COMMAND cp -p <SOURCE_DIR>/mpeu/Makefile mpeu/
   )
+if (USE_MPI_SERIAL)
+  ExternalProject_add_step(mct_project copy_mpi_serial_files
+    DEPENDEES configure
+    DEPENDERS build
+    WORKING_DIRECTORY <BINARY_DIR>
+    COMMAND mkdir -p mpi-serial
+    COMMAND cp -p <SOURCE_DIR>/mpi-serial/Makefile mpi-serial/
+    COMMAND cp <SOURCE_DIR>/mpi-serial/mpif.h mpi-serial/
+    COMMAND cp <SOURCE_DIR>/mpi-serial/mpi.h mpi-serial/
+    )
+endif()
 
 # Tell cmake to look for libraries & mod files here, because this is where we built libraries
 include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mct)
 include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
 link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mct)
 link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
+if (USE_MPI_SERIAL)
+  include_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpi-serial)
+  link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpi-serial)
+endif()
 
 # ------------------------------------------------------------------------
 # Done MCT build
@@ -58,14 +82,14 @@ link_directories(${CMAKE_CURRENT_BINARY_DIR}/mct/mpeu)
 
 # csm_share (we don't build it here because it seems to be built differently
 # by different tests?)
-set(SHARE_ROOT "${CIME_ROOT}/share/csm_share")
-add_subdirectory(${SHARE_ROOT}/shr csm_share)
+set(SHARE_ROOT "${CIME_ROOT}/src/share")
+add_subdirectory(${SHARE_ROOT}/util csm_share)
 include_directories(${SHARE_ROOT}/include)
 
 # esmf_wrf_timemgr not built here because it depends on csm_share.
-add_subdirectory(${CIME_ROOT}/share/esmf_wrf_timemgr esmf_wrf_timemgr)
-include_directories(${CIME_ROOT}/share/esmf_wrf_timemgr)
+add_subdirectory(${SHARE_ROOT}/esmf_wrf_timemgr esmf_wrf_timemgr)
+include_directories(${SHARE_ROOT}/esmf_wrf_timemgr)
 
 # Now the actual test directories.
-add_subdirectory(driver_cpl/unit_test)
-add_subdirectory(share/csm_share/test/unit)
+add_subdirectory(${CIME_ROOT}/src/drivers/mct/unit_test)
+add_subdirectory(${SHARE_ROOT}/test/unit)