Merge pull request #106 from climbfuji/update_gsl_develop_from_main_2…

…0210921

Update gsl/develop from main 2021/09/21

CMakeLists.txt

@@ -7,9 +7,9 @@ endif (NOT PROJECT)
 #------------------------------------------------------------------------------
 cmake_minimum_required(VERSION 3.0)
 
-project(ccppphys
-        VERSION 4.0.0
-        LANGUAGES C CXX Fortran)
+project(ccpp_physics
+        VERSION 5.0.0
+        LANGUAGES Fortran)
 
 # Use rpaths on MacOSX
 set(CMAKE_MACOSX_RPATH 1)
@@ -31,25 +31,9 @@ set(AUTHORS "Grant Firl" "Dom Heinzeller" "Man Zhang" "Laurie Carson")
 if (OPENMP)
   include(detect_openmp)
   detect_openmp()
-  #set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-  #set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-  #set (CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${OpenMP_Fortran_FLAGS}")
-  message(STATUS "Enable OpenMP support for C/C++/Fortran compiler")
+  message(STATUS "Enable OpenMP support")
 else (OPENMP)
-  message (STATUS "Disable OpenMP support for C/C++/Fortran compiler")
-endif()
-
-#------------------------------------------------------------------------------
-# The Fortran compiler/linker flag inserted by cmake to create shared libraries
-# with the Intel compiler is deprecated (-i_dynamic), correct here.
-# CMAKE_Fortran_COMPILER_ID = {"Intel", "PGI", "GNU", "Clang", "MSVC", ...}
-if ("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel")
-    string(REPLACE "-i_dynamic" "-shared-intel"
-           CMAKE_SHARED_LIBRARY_CREATE_Fortran_FLAGS
-           "${CMAKE_SHARED_LIBRARY_CREATE_Fortran_FLAGS}")
-    string(REPLACE "-i_dynamic" "-shared-intel"
-           CMAKE_SHARED_LIBRARY_LINK_Fortran_FLAGS
-           "${CMAKE_SHARED_LIBRARY_LINK_Fortran_FLAGS}")
+  message (STATUS "Disable OpenMP support")
 endif()
 
 #------------------------------------------------------------------------------
@@ -321,22 +305,8 @@ else()
   message (FATAL_ERROR "This program has only been compiled with gfortran, pgf90 and ifort. If another compiler is needed, the appropriate flags must be added in ${GFS_PHYS_SRC}/CMakeLists.txt")
 endif()
 
-# The auto-generated caps can contain calls to physics schemes in
-# which some of the arguments (pointers, arrays) are not associated/allocated.
-# This is on purpose to avoid allocating fields that are not used inside the
-# scheme if, for example, certain conditions are not met. To avoid
-# Fortran runtime errors, it is necessary to remove checks for pointers
-# that are not associated and for array bounds from the caps ONLY. For the
-# physics schemes, these checks can and should remain enabled. Overwriting
-# the pointer check flags explicitly works for Intel and GNU, but not for PGI.
-if (${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
-  set_property(SOURCE ${CAPS} APPEND_STRING PROPERTY COMPILE_FLAGS " -fcheck=no-pointer,no-bounds ")
-elseif (${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
-  set_property(SOURCE ${CAPS} APPEND_STRING PROPERTY COMPILE_FLAGS " -check nopointers,nobounds ")
-endif ()
-
 #------------------------------------------------------------------------------
-add_library(ccppphys STATIC ${SCHEMES} ${SCHEMES_SFX_OPT} ${CAPS})
+add_library(ccpp_physics STATIC ${SCHEMES} ${SCHEMES_SFX_OPT} ${CAPS})
 # Generate list of Fortran modules from defined sources
 foreach(source_f90 ${CAPS})
     get_filename_component(tmp_source_f90 ${source_f90} NAME)
@@ -345,20 +315,25 @@ foreach(source_f90 ${CAPS})
     list(APPEND MODULES_F90 ${CMAKE_CURRENT_BINARY_DIR}/${module_f90})
 endforeach()
 
-set_target_properties(ccppphys PROPERTIES VERSION ${PROJECT_VERSION}
+set_target_properties(ccpp_physics PROPERTIES VERSION ${PROJECT_VERSION}
                                      SOVERSION ${PROJECT_VERSION_MAJOR})
 
+target_include_directories(ccpp_physics PUBLIC
+                           $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>)
+
+target_link_libraries(ccpp_physics PUBLIC w3nco::w3nco_d NetCDF::NetCDF_Fortran)
+
 if (PROJECT STREQUAL "CCPP-FV3")
   # Define where to install the library
-  install(TARGETS ccppphys
-          EXPORT ccppphys-targets
+  install(TARGETS ccpp_physics
+          EXPORT ccpp_physics-targets
           ARCHIVE DESTINATION lib
           LIBRARY DESTINATION lib
           RUNTIME DESTINATION lib
   )
   # Export our configuration
-  install(EXPORT ccppphys-targets
-          FILE ccppphys-config.cmake
+  install(EXPORT ccpp_physics-targets
+          FILE ccpp_physics-config.cmake
           DESTINATION lib/cmake
   )
   # Define where to install the C headers and Fortran modules

physics/GFS_DCNV_generic.meta

@@ -267,7 +267,7 @@
   standard_name = convective_transportable_tracers
   long_name = array to contain cloud water and other convective trans. tracers
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_tracers_for_convective_transport)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_tracers_for_convective_transport)
   type = real
   kind = kind_phys
   intent = in
@@ -477,7 +477,7 @@
   standard_name = cumulative_change_of_state_variables
   long_name = diagnostic tendencies for state variables
   units = various
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_cumulative_change_processes)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_cumulative_change_processes)
   type = real
   kind = kind_phys
   intent = inout
@@ -534,7 +534,7 @@
   standard_name = tracer_concentration_of_new_state
   long_name = tracer concentration updated by physics
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_tracers)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_tracers)
   type = real
   kind = kind_phys
   intent = in
@@ -543,7 +543,7 @@
   standard_name = tracer_concentration_save
   long_name = tracer concentration before entering a physics scheme
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_tracers)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_tracers)
   type = real
   kind = kind_phys
   intent = in
@@ -778,7 +778,7 @@
   standard_name = convective_transportable_tracers
   long_name = array to contain cloud water and other convective trans. tracers
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_tracers_for_convective_transport)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_tracers_for_convective_transport)
   type = real
   kind = kind_phys
   intent = in

physics/GFS_MP_generic.meta

@@ -823,7 +823,7 @@
   standard_name = cumulative_change_of_state_variables
   long_name = diagnostic tendencies for state variables
   units = various
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_cumulative_change_processes)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_cumulative_change_processes)
   type = real
   kind = kind_phys
   intent = inout
@@ -832,7 +832,7 @@
   standard_name = cumulative_change_of_state_variables_outer_index
   long_name = index of state-variable and process in last dimension of diagnostic tendencies array AKA cumulative_change_index
   units = index
-  dimensions = (number_of_tracers_plus_one_hundred,number_of_causes)
+  dimensions = (number_of_tracers_plus_one_hundred,number_of_cumulative_change_processes)
   type = integer
   intent = in
   optional = F

physics/GFS_PBL_generic.meta

@@ -820,7 +820,7 @@
   standard_name = cumulative_change_of_state_variables
   long_name = diagnostic tendencies for state variables
   units = various
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_cumulative_change_processes)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_cumulative_change_processes)
   type = real
   kind = kind_phys
   intent = inout

physics/GFS_SCNV_generic.meta

@@ -259,7 +259,7 @@
   standard_name = convective_transportable_tracers
   long_name = array to contain cloud water and other convective trans. tracers
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_tracers_for_convective_transport)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_tracers_for_convective_transport)
   type = real
   kind = kind_phys
   intent = in

physics/GFS_rrtmg_pre.meta

@@ -604,7 +604,7 @@
   standard_name = surface_stochastic_weights_from_coupled_process
   long_name = weights for stochastic surface physics perturbation
   units = none
-  dimensions = (horizontal_loop_extent,number_of_surface_perturbations)
+  dimensions = (horizontal_loop_extent,number_of_perturbed_land_surface_variables)
   type = real
   kind = kind_phys
   intent = in

physics/GFS_suite_interstitial.meta

@@ -1605,7 +1605,7 @@
   standard_name = liquid_cloud_number_concentration_save
   long_name = liquid cloud number concentration before entering a physics scheme
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   intent = inout
@@ -1614,7 +1614,7 @@
   standard_name = ice_cloud_number_concentration_save
   long_name = ice cloud number concentration before entering a physics scheme
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   intent = inout
@@ -1886,7 +1886,7 @@
   standard_name = liquid_cloud_number_concentration_save
   long_name = liquid cloud number concentration before entering a physics scheme
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   intent = in
@@ -1895,7 +1895,7 @@
   standard_name = ice_cloud_number_concentration_save
   long_name = ice cloud number concentration before entering a physics scheme
   units = kg kg-1
-  dimensions = (horizontal_loop_extent,vertical_dimension)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
   type = real
   kind = kind_phys
   intent = in
@@ -1993,7 +1993,7 @@
   standard_name = cumulative_change_of_state_variables
   long_name = diagnostic tendencies for state variables
   units = various
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_cumulative_change_processes)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_cumulative_change_processes)
   type = real
   kind = kind_phys
   intent = inout

physics/drag_suite.meta

@@ -649,7 +649,7 @@
   standard_name = cumulative_change_of_state_variables
   long_name = diagnostic tendencies for state variables
   units = various
-  dimensions = (horizontal_loop_extent,vertical_dimension,number_of_cumulative_change_processes)
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension,number_of_cumulative_change_processes)
   type = real
   kind = kind_phys
   active = (flag_for_diagnostics_3D)

physics/sfcsub.F

@@ -2019,12 +2019,14 @@ subroutine sfccycle(lugb,len,lsoil,sig1t,deltsfc                    &
 !    *,' tsffcs=',tsffcs(iprnt),' slianl=',slianl(iprnt)
 
       do i=1,len
+       if (nint(slmskl(i)) /= 1) then
         if (sicanl(i) >= min_ice(i)) then
           slianl(i) = 2.0_kind_io8
         else
           slianl(i) = zero
           sicanl(i) = zero
         endif
+       endif
       enddo
 
       if (fh-deltsfc > -0.001 ) then