Merge branch 'develop' of https://github.com/NOAA-EMC/fv3atm into tim…

…estep_init_final
NOAA-EMC · junwang-noaa · Jan 14, 2021 · Dec 18, 2020 · Dec 18, 2020 · Dec 18, 2020
commit 98f5cbaced52765c2e830283a8d7159b2ca40c11
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,13 +1,18 @@
 if(CCPP)
 
+  if(DEBUG)
+    set(_ccpp_debug_arg "--debug")
+  endif()
   if(DEFINED CCPP_SUITES)
     set(_ccpp_suites_arg "--suites=${CCPP_SUITES}")
+    message("Calling CCPP code generator (ccpp_prebuild.py) for suites ${_ccpp_suites_arg} ...")
+  else()
+    message("Calling CCPP code generator (ccpp_prebuild.py) for all available suites ...")
   endif()
-  message("Calling CCPP code generator (ccpp_prebuild.py) ... ${_ccpp_suites_arg}")
   execute_process(COMMAND ${Python_EXECUTABLE}
                           "ccpp/framework/scripts/ccpp_prebuild.py"
                           "--config=ccpp/config/ccpp_prebuild_config.py"
-                          "--builddir=${CMAKE_CURRENT_BINARY_DIR}" ${_ccpp_suites_arg}
+                          "--builddir=${CMAKE_CURRENT_BINARY_DIR}" ${_ccpp_suites_arg} ${_ccpp_debug_arg}
                   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
                   OUTPUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/ccpp_prebuild.out
                   ERROR_FILE  ${CMAKE_CURRENT_BINARY_DIR}/ccpp_prebuild.err
@@ -136,8 +141,8 @@ if(CCPP)
   add_dependencies(ccppphys ccpp)
   target_include_directories(fv3dycore PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/ccpp/framework/src
                                                ${CMAKE_CURRENT_BINARY_DIR}/ccpp/driver)
-  target_link_libraries(ccppphys PRIVATE sp::sp_d
-                                         w3nco::w3nco_d)
+  target_link_libraries(ccppphys PUBLIC sp::sp_d
+                                        w3nco::w3nco_d)
 endif()
 
 ###############################################################################

diff --git a/atmos_model.F90 b/atmos_model.F90
@@ -100,7 +100,7 @@ module atmos_model_mod
 use IPD_driver,         only: IPD_initialize, IPD_initialize_rst
 use CCPP_driver,        only: CCPP_step, non_uniform_blocks
 
-use stochastic_physics_wrapper_mod, only: stochastic_physics_wrapper
+use stochastic_physics_wrapper_mod, only: stochastic_physics_wrapper,stochastic_physics_wrapper_end
 #else
 use IPD_driver,         only: IPD_initialize, IPD_initialize_rst, IPD_step
 use physics_abstraction_layer, only: time_vary_step, radiation_step1, physics_step1, physics_step2
@@ -970,6 +970,9 @@ subroutine atmos_model_end (Atmos)
 !---- termination routine for atmospheric model ----
 
     call atmosphere_end (Atmos % Time, Atmos%grid, restart_endfcst)
+
+    call stochastic_physics_wrapper_end(IPD_Control)
+
     if(restart_endfcst) then
       call FV3GFS_restart_write (IPD_Data, IPD_Restart, Atm_block, &
                                  IPD_Control, Atmos%domain)
@@ -1769,7 +1772,6 @@ subroutine assign_importdata(rc)
                   nb = Atm_block%blkno(i,j)
                   ix = Atm_block%ixp(i,j)
 
-                  IPD_Data(nb)%Sfcprop%fice(ix)          = zero
                   IPD_Data(nb)%Coupling%slimskin_cpl(ix) = IPD_Data(nb)%Sfcprop%slmsk(ix)
                   ofrac = IPD_Data(nb)%Sfcprop%oceanfrac(ix)
                   if (ofrac > zero) then
@@ -1784,7 +1786,7 @@ subroutine assign_importdata(rc)
                       if (abs(one-ofrac) < epsln) then
                         IPD_Data(nb)%Sfcprop%slmsk(ix)         = zero
                         IPD_Data(nb)%Coupling%slimskin_cpl(ix) = zero
-                      end if
+                      endif
                     endif
                   endif
                 enddo

diff --git a/ccpp/config/ccpp_prebuild_config.py b/ccpp/config/ccpp_prebuild_config.py
@@ -113,6 +113,8 @@
     'ccpp/physics/physics/GFS_time_vary_pre.fv3.F90',
     'ccpp/physics/physics/cires_ugwp.F90',
     'ccpp/physics/physics/cires_ugwp_post.F90',
+    'ccpp/physics/physics/unified_ugwp.F90',
+    'ccpp/physics/physics/unified_ugwp_post.F90',
     'ccpp/physics/physics/cnvc90.f',
     'ccpp/physics/physics/cs_conv.F90',
     'ccpp/physics/physics/cs_conv_aw_adj.F90',
@@ -159,6 +161,7 @@
     'ccpp/physics/physics/ozphys_2015.f',
     'ccpp/physics/physics/precpd.f',
     'ccpp/physics/physics/phys_tend.F90',
+    'ccpp/physics/physics/tracer_sanitizer.F90',
     'ccpp/physics/physics/radlw_main.F90',
     'ccpp/physics/physics/radsw_main.F90',
     'ccpp/physics/physics/rascnv.F90',
@@ -200,8 +203,10 @@
     'ccpp/physics/physics/rrtmgp_lw_cloud_sampling.F90',
     'ccpp/physics/physics/rrtmgp_sw_cloud_sampling.F90',
     'ccpp/physics/physics/GFS_cloud_diagnostics.F90',
+    'ccpp/physics/physics/GFS_rrtmgp_thompsonmp_pre.F90',
     'ccpp/physics/physics/GFS_rrtmgp_gfdlmp_pre.F90',
     'ccpp/physics/physics/GFS_rrtmgp_zhaocarr_pre.F90',
+    'ccpp/physics/physics/GFS_rrtmgp_cloud_overlap_pre.F90',
     'ccpp/physics/physics/GFS_rrtmgp_sw_post.F90'
     ]
 
@@ -296,12 +301,6 @@
             'rime_factor',
             ],
         },
-    'rrtmgp_lw_rte' : {
-         'rrtmgp_lw_rte_run' : [
-             'RRTMGP_jacobian_of_lw_flux_profile_upward',
-             'RRTMGP_jacobian_of_lw_flux_profile_downward',
-             ],
-         },
     'rrtmgp_sw_rte' : {
          'rrtmgp_sw_rte_run' : [
              'components_of_surface_downward_shortwave_fluxes',
@@ -318,12 +317,6 @@
              'tendency_of_air_temperature_due_to_longwave_heating_assuming_clear_sky_on_radiation_time_step',
              ],
          },
-    'GFS_suite_interstitial_2' : {
-         'GFS_suite_interstitial_2_run' : [
-             'RRTMGP_jacobian_of_lw_flux_profile_upward',
-             'RRTMGP_lw_flux_profile_upward_allsky',
-             ],
-         },
     #'subroutine_name_1' : 'all',
     #'subroutine_name_2' : 'none',
     #'subroutine_name_2' : [ 'var1', 'var3'],

diff --git a/ccpp/suites/suite_FV3_GFS_v15p2_RRTMGP.xml b/ccpp/suites/suite_FV3_GFS_v15p2_RRTMGP.xml
@@ -20,6 +20,7 @@
       <scheme>GFS_suite_interstitial_rad_reset</scheme>
       <scheme>GFS_rrtmgp_pre</scheme>
       <scheme>GFS_rrtmgp_gfdlmp_pre</scheme>
+      <scheme>GFS_rrtmgp_cloud_overlap_pre</scheme>
       <scheme>GFS_cloud_diagnostics</scheme>
       <scheme>GFS_rrtmgp_sw_pre</scheme>
       <scheme>rrtmgp_sw_gas_optics</scheme>

diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_RRTMGP.xml b/ccpp/suites/suite_FV3_GFS_v16beta_RRTMGP.xml
@@ -20,6 +20,7 @@
       <scheme>GFS_suite_interstitial_rad_reset</scheme>
       <scheme>GFS_rrtmgp_pre</scheme>
       <scheme>GFS_rrtmgp_gfdlmp_pre</scheme>
+      <scheme>GFS_rrtmgp_cloud_overlap_pre</scheme>
       <scheme>GFS_cloud_diagnostics</scheme>
       <scheme>GFS_rrtmgp_sw_pre</scheme>
       <scheme>rrtmgp_sw_gas_optics</scheme>

diff --git a/ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml b/ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml
@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<suite name="FV3_GFS_v16beta_coupled" version="1">
+  <!-- <init></init> -->
+  <group name="fast_physics">
+    <subcycle loop="1">
+      <scheme>fv_sat_adj</scheme>
+    </subcycle>
+  </group>
+  <group name="time_vary">
+    <subcycle loop="1">
+      <scheme>GFS_time_vary_pre</scheme>
+      <scheme>GFS_rrtmg_setup</scheme>
+      <scheme>GFS_rad_time_vary</scheme>
+      <scheme>GFS_phys_time_vary</scheme>
+    </subcycle>
+  </group>
+  <group name="radiation">
+    <subcycle loop="1">
+      <scheme>GFS_suite_interstitial_rad_reset</scheme>
+      <scheme>GFS_rrtmg_pre</scheme>
+      <scheme>rrtmg_sw_pre</scheme>
+      <scheme>rrtmg_sw</scheme>
+      <scheme>rrtmg_sw_post</scheme>
+      <scheme>rrtmg_lw_pre</scheme>
+      <scheme>rrtmg_lw</scheme>
+      <scheme>rrtmg_lw_post</scheme>
+      <scheme>GFS_rrtmg_post</scheme>
+    </subcycle>
+  </group>
+  <group name="physics">
+    <subcycle loop="1">
+      <scheme>GFS_suite_interstitial_phys_reset</scheme>
+      <scheme>GFS_suite_stateout_reset</scheme>
+      <scheme>get_prs_fv3</scheme>
+      <scheme>GFS_suite_interstitial_1</scheme>
+      <scheme>GFS_surface_generic_pre</scheme>
+      <scheme>GFS_surface_composites_pre</scheme>
+      <scheme>dcyc2t3</scheme>
+      <scheme>GFS_surface_composites_inter</scheme>
+      <scheme>GFS_suite_interstitial_2</scheme>
+    </subcycle>
+    <!-- Surface iteration loop -->
+    <subcycle loop="2">
+      <scheme>sfc_diff</scheme>
+      <scheme>GFS_surface_loop_control_part1</scheme>
+      <scheme>sfc_ocean</scheme>
+      <scheme>lsm_noah</scheme>
+      <scheme>sfc_cice</scheme>
+      <scheme>sfc_sice</scheme>
+      <scheme>GFS_surface_loop_control_part2</scheme>
+    </subcycle>
+    <!-- End of surface iteration loop -->
+    <subcycle loop="1">
+      <scheme>GFS_surface_composites_post</scheme>
+      <scheme>sfc_diag</scheme>
+      <scheme>sfc_diag_post</scheme>
+      <scheme>GFS_surface_generic_post</scheme>
+      <scheme>GFS_PBL_generic_pre</scheme>
+      <scheme>satmedmfvdifq</scheme>
+      <scheme>GFS_PBL_generic_post</scheme>
+      <scheme>GFS_GWD_generic_pre</scheme>
+      <scheme>cires_ugwp</scheme>
+      <scheme>cires_ugwp_post</scheme>
+      <scheme>GFS_GWD_generic_post</scheme>
+      <scheme>rayleigh_damp</scheme>
+      <scheme>GFS_suite_stateout_update</scheme>
+      <scheme>ozphys_2015</scheme>
+      <scheme>h2ophys</scheme>
+      <scheme>get_phi_fv3</scheme>
+      <scheme>GFS_suite_interstitial_3</scheme>
+      <scheme>GFS_DCNV_generic_pre</scheme>
+      <scheme>samfdeepcnv</scheme>
+      <scheme>GFS_DCNV_generic_post</scheme>
+      <scheme>GFS_SCNV_generic_pre</scheme>
+      <scheme>samfshalcnv</scheme>
+      <scheme>GFS_SCNV_generic_post</scheme>
+      <scheme>GFS_suite_interstitial_4</scheme>
+      <scheme>cnvc90</scheme>
+      <scheme>GFS_MP_generic_pre</scheme>
+      <scheme>gfdl_cloud_microphys</scheme>
+      <scheme>GFS_MP_generic_post</scheme>
+      <scheme>maximum_hourly_diagnostics</scheme>
+    </subcycle>
+  </group>
+  <group name="stochastics">
+    <subcycle loop="1">
+      <scheme>GFS_stochastics</scheme>
+      <scheme>phys_tend</scheme>
+    </subcycle>
+  </group>
+  <!-- <finalize></finalize> -->
+</suite>
diff --git a/ccpp/suites/suite_FV3_GSD_noah.xml b/ccpp/suites/suite_FV3_GSD_noah.xml
@@ -79,6 +79,7 @@
       <scheme>mp_thompson_post</scheme>
       <scheme>GFS_MP_generic_post</scheme>
       <scheme>cu_gf_driver_post</scheme>
+      <!-- <scheme>tracer_sanitizer</scheme> -->
       <scheme>maximum_hourly_diagnostics</scheme>
     </subcycle>
   </group>

diff --git a/ccpp/suites/suite_FV3_GSD_v0.xml b/ccpp/suites/suite_FV3_GSD_v0.xml
@@ -81,6 +81,7 @@
       <scheme>mp_thompson_post</scheme>
       <scheme>GFS_MP_generic_post</scheme>
       <scheme>cu_gf_driver_post</scheme>
+      <!-- <scheme>tracer_sanitizer</scheme> -->
       <scheme>maximum_hourly_diagnostics</scheme>
     </subcycle>
   </group>

diff --git a/ccpp/suites/suite_FV3_GSD_v0_RRTMGP.xml b/ccpp/suites/suite_FV3_GSD_v0_RRTMGP.xml
@@ -0,0 +1,104 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<suite name="FV3_GSD_v0_RRTMGP" version="1">
+  <!-- <init></init> -->
+  <group name="time_vary">
+    <subcycle loop="1">
+      <scheme>GFS_time_vary_pre</scheme>
+      <scheme>GFS_rrtmgp_setup</scheme>
+      <scheme>GFS_rad_time_vary</scheme>
+      <scheme>GFS_phys_time_vary</scheme>
+    </subcycle>
+  </group>
+  <group name="radiation">
+    <subcycle loop="1">
+      <scheme>GFS_suite_interstitial_rad_reset</scheme>
+      <scheme>sgscloud_radpre</scheme>
+      <scheme>GFS_rrtmgp_pre</scheme>
+      <scheme>GFS_rrtmgp_thompsonmp_pre</scheme>
+      <scheme>GFS_rrtmgp_cloud_overlap_pre</scheme>
+      <scheme>GFS_cloud_diagnostics</scheme>
+      <scheme>GFS_rrtmgp_sw_pre</scheme>
+      <scheme>rrtmgp_sw_gas_optics</scheme>
+      <scheme>rrtmgp_sw_aerosol_optics</scheme>
+      <scheme>rrtmgp_sw_cloud_optics</scheme>
+      <scheme>rrtmgp_sw_cloud_sampling</scheme>
+      <scheme>rrtmgp_sw_rte</scheme>
+      <scheme>GFS_rrtmgp_sw_post</scheme>
+      <scheme>rrtmgp_lw_pre</scheme>
+      <scheme>rrtmgp_lw_gas_optics</scheme>
+      <scheme>rrtmgp_lw_aerosol_optics</scheme>
+      <scheme>rrtmgp_lw_cloud_optics</scheme>
+      <scheme>rrtmgp_lw_cloud_sampling</scheme>
+      <scheme>rrtmgp_lw_rte</scheme>
+      <scheme>sgscloud_radpost</scheme>
+      <scheme>GFS_rrtmgp_lw_post</scheme> 
+    </subcycle>
+  </group>
+  <group name="physics">
+    <subcycle loop="1">
+      <scheme>GFS_suite_interstitial_phys_reset</scheme>
+      <scheme>GFS_suite_stateout_reset</scheme>
+      <scheme>get_prs_fv3</scheme>
+      <scheme>GFS_suite_interstitial_1</scheme>
+      <scheme>GFS_surface_generic_pre</scheme>
+      <scheme>GFS_surface_composites_pre</scheme>
+      <scheme>dcyc2t3</scheme>
+      <scheme>GFS_surface_composites_inter</scheme>
+      <scheme>GFS_suite_interstitial_2</scheme>
+    </subcycle>
+    <!-- Surface iteration loop -->
+    <subcycle loop="2">
+      <scheme>sfc_diff</scheme>
+      <scheme>GFS_surface_loop_control_part1</scheme>
+      <scheme>sfc_nst_pre</scheme>
+      <scheme>sfc_nst</scheme>
+      <scheme>sfc_nst_post</scheme>
+      <scheme>lsm_ruc</scheme>
+      <scheme>lsm_ruc_sfc_sice_pre</scheme>
+      <scheme>sfc_sice</scheme>
+      <scheme>lsm_ruc_sfc_sice_post</scheme>
+      <scheme>GFS_surface_loop_control_part2</scheme>
+    </subcycle>
+    <!-- End of surface iteration loop -->
+    <subcycle loop="1">
+      <scheme>GFS_surface_composites_post</scheme>
+      <scheme>sfc_diag</scheme>
+      <scheme>sfc_diag_post</scheme>
+      <scheme>GFS_surface_generic_post</scheme>
+      <scheme>mynnedmf_wrapper</scheme>
+      <scheme>GFS_GWD_generic_pre</scheme>
+      <scheme>cires_ugwp</scheme>
+      <scheme>cires_ugwp_post</scheme>
+      <scheme>GFS_GWD_generic_post</scheme>
+      <scheme>rayleigh_damp</scheme>
+      <scheme>GFS_suite_stateout_update</scheme>
+      <scheme>ozphys_2015</scheme>
+      <scheme>h2ophys</scheme>
+      <scheme>get_phi_fv3</scheme>
+      <scheme>GFS_suite_interstitial_3</scheme>
+      <scheme>GFS_DCNV_generic_pre</scheme>
+      <scheme>cu_gf_driver_pre</scheme>
+      <scheme>cu_gf_driver</scheme>
+      <scheme>GFS_DCNV_generic_post</scheme>
+      <scheme>GFS_SCNV_generic_pre</scheme>
+      <scheme>GFS_SCNV_generic_post</scheme>
+      <scheme>GFS_suite_interstitial_4</scheme>
+      <scheme>cnvc90</scheme>
+      <scheme>GFS_MP_generic_pre</scheme>
+      <scheme>mp_thompson_pre</scheme>
+      <scheme>mp_thompson</scheme>
+      <scheme>mp_thompson_post</scheme>
+      <scheme>GFS_MP_generic_post</scheme>
+      <scheme>cu_gf_driver_post</scheme>
+      <scheme>maximum_hourly_diagnostics</scheme>
+    </subcycle>
+  </group>
+  <group name="stochastics">
+    <subcycle loop="1">
+      <scheme>GFS_stochastics</scheme>
+      <scheme>phys_tend</scheme>
+    </subcycle>
+  </group>
+  <!-- <finalize></finalize> -->
+</suite>