Merge seaice/develop into cice/icebergs

README.md

@@ -1,4 +1,4 @@
-MPAS-v5.2
+MPAS-v6.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

src/core_atmosphere/Makefile

@@ -34,7 +34,7 @@ physcore: mpas_atm_dimensions.o
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_wrf/files/*TBL .)
 	( cd ../..; ln -sf ./src/core_atmosphere/physics/physics_wrf/files/*DATA* .)
 
-dycore: mpas_atm_dimensions.o
+dycore: mpas_atm_dimensions.o physcore
 	( cd dynamics; $(MAKE) all PHYSICS="$(PHYSICS)" )
 
 diagcore: physcore dycore
@@ -48,7 +48,7 @@ atmcore: physcore dycore diagcore $(OBJS)
 
 mpas_atm_core_interface.o: mpas_atm_core.o
 
-mpas_atm_core.o: dycore mpas_atm_threading.o
+mpas_atm_core.o: dycore diagcore mpas_atm_threading.o
 
 mpas_atm_dimensions.o:
 

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="5.2">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="6.0">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -429,14 +429,13 @@
 			<var name="defc_b"/>
 			<var name="coeffs_reconstruct"/>
 			<var_array name="scalars"/>
+			<var name="initial_time"/>
 			<var name="xtime"/>
 			<var name="u"/>
 			<var name="w"/>
 			<var name="rho"/>
 			<var name="theta"/>
 			<var name="relhum"/>
-			<var name="exner_base"/>
-			<var name="pressure_base"/>
 			<var name="rho_base"/>
 			<var name="theta_base"/>
 			<var name="surface_pressure"/>
@@ -563,6 +562,7 @@
 			<var name="re_snow" packages="mp_thompson_in;mp_wsm6_in"/>
 			<var name="nt_c" packages="mp_thompson_in"/>
 			<var name="mu_c" packages="mp_thompson_in"/>
+			<var name="initial_time"/>
 			<var name="xtime"/>
 			<var name="u"/>
 			<var name="w"/>
@@ -845,6 +845,7 @@
 			<var name="fzm"/>
 			<var name="fzp"/>
 			<var name="zz"/>
+			<var name="initial_time"/>
 			<var name="xtime"/>
 			<var name="u"/>
 			<var name="w"/>
@@ -924,6 +925,7 @@
                         output_interval="3:00:00"
                         runtime_format="separate_file">
 
+			<var name="initial_time"/>
 			<var name="xtime"/>
 			<var name="olrtoa"/>
 			<var name="rainc"/>
@@ -1299,14 +1301,13 @@
 
                 <var name="north" type="real" dimensions="R3 nCells" units="unitless"
                      description="Cartesian components of the unit vector pointing north"/>
-
-                <!-- Arrays needed only in the CAM LW and SW radiation codes: Aerosols -->
-                <var name="m_hybi" type="real" dimensions="nAerLevels nCells" units="unitless"
-                     description="Matched hybi (needs to be re-checked)"/>
         </var_struct>
 
         <var_struct name="state" time_levs="2">
 
+                <var name="initial_time" type="text" dimensions="" units="YYYY-MM-DD_hh:mm:ss"
+                     description="Model initialization time"/>
+
                 <var name="xtime" type="text" dimensions="Time" units="YYYY-MM-DD_hh:mm:ss"
                      description="Model valid time"/>
 
@@ -1323,9 +1324,6 @@
                 <var name="theta_m" type="real" dimensions="nVertLevels nCells Time" units="K"
                      description="Moist potential temperature: theta*(1+q_v*R_v/R_d)"/>
 
-                <var name="m_ps" type="real" dimensions="nCells Time" units="Pa"
-                     description="Surface pressure from match on MPAS grid"/>
-
                 <var_array name="scalars" type="real" dimensions="nVertLevels nCells Time">
                         <var name="qv" array_group="moist" units="kg kg^{-1}"
                              description="Water vapor mixing ratio"/>
@@ -1633,35 +1631,35 @@
 
                 <!-- scalar tendencies -->
                 <var_array name="scalars_tend" type="real" dimensions="nVertLevels nCells Time">
-                        <var name="tend_qv" name_in_code="qv" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of water vapor mixing ratio"/>
+                        <var name="tend_qv" name_in_code="qv" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of water vapor mass per unit volume divided by d(zeta)/dz"/>
 
-                        <var name="tend_qc" name_in_code="qc" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of cloud water mixing ratio"
+                        <var name="tend_qc" name_in_code="qc" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of cloud water mass per unit volume divided by d(zeta)/dz"
                              packages="bl_mynn_in;bl_ysu_in;cu_tiedtke_in;mp_kessler_in;mp_thompson_in;mp_wsm6_in"/>
 
-                        <var name="tend_qr" name_in_code="qr" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of rain water mixing ratio"
+                        <var name="tend_qr" name_in_code="qr" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of rain water mass per unit volume divided by d(zeta)/dz"
                              packages="mp_kessler_in;mp_thompson_in;mp_wsm6_in"/>
 
-                        <var name="tend_qi" name_in_code="qi" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of ice mixing ratio"
+                        <var name="tend_qi" name_in_code="qi" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of ice mass per unit volume divided by d(zeta)/dz"
                              packages="bl_mynn_in;bl_ysu_in;cu_tiedtke_in;mp_thompson_in;mp_wsm6_in"/>
 
-                        <var name="tend_qs" name_in_code="qs" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of snow ratio"
+                        <var name="tend_qs" name_in_code="qs" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of snow mass per unit volume divided by d(zeta)/dz"
                              packages="mp_thompson_in;mp_wsm6_in"/>
 
-                        <var name="tend_qg" name_in_code="qg" array_group="moist" units="kg kg^{-1} s^{-1}"
-                             description="Tendency of graupel mixing ratio"
+                        <var name="tend_qg" name_in_code="qg" array_group="moist" units="kg m^{-3} s^{-1}"
+                             description="Tendency of graupel mass per unit volume divided by d(zeta)/dz"
                              packages="mp_thompson_in;mp_wsm6_in"/>
 
-                        <var name="tend_ni" name_in_code="ni" array_group="number" units="nb kg^{-1} s^{-1}"
-                             description="Tendency of cloud ice number concentration"
+                        <var name="tend_ni" name_in_code="ni" array_group="number" units="nb m^{-3} s^{-1}"
+                             description="Tendency of cloud ice number concentration multiplied by dry air density divided by d(zeta)/dz"
                              packages="bl_mynn_in;mp_thompson_in"/>
 
-                        <var name="tend_nr" name_in_code="nr" array_group="number" units="nb kg^{-1} s^{-1}" 
-                             description="Tendency of rain number concentration"
+                        <var name="tend_nr" name_in_code="nr" array_group="number" units="nb m^{-3} s^{-1}" 
+                             description="Tendency of rain number concentration multiplied by dry air density divided by d(zeta)/dz"
                              packages="mp_thompson_in"/>
                 </var_array>
         </var_struct>
@@ -2547,6 +2545,12 @@
                 <!-- ... ADDITIONAL "RADIATION" ARRAYS NEEDED ONLY IN THE "CAM" LW AND SW RADIATION CODES:              -->
                 <!-- ================================================================================================== -->
 
+                <var name="m_hybi" type="real" dimensions="nAerLevels nCells" units="unitless"
+                     description="Matched hybi (needs to be re-checked)"/>
+
+                <var name="m_ps" type="real" dimensions="nCells Time" units="Pa"
+                     description="Surface pressure from match on MPAS grid"/>
+
                 <!-- INFRARED ABSORPTION: -->
                 <var name="absnxt" type="real" dimensions="nVertLevels cam_dim1 nCells Time" units="-"
                      description="Total nearest layer absorptivity"/>

src/core_atmosphere/dynamics/mpas_atm_time_integration.F

@@ -394,7 +394,7 @@ subroutine atm_srk3(domain, dt, itimestep)
       call mpas_timer_stop('atm_compute_moist_coefficients')
 
 #ifdef DO_PHYSICS
-      call mpas_timer_start('physics_addtend')
+      call mpas_timer_start('physics_get_tend')
       block => domain % blocklist
       do while (associated(block))
          call mpas_pool_get_subpool(block % structs, 'mesh', mesh)
@@ -418,7 +418,7 @@ subroutine atm_srk3(domain, dt, itimestep)
                      tend_rho_physics )
          block => block % next
       end do
-      call mpas_timer_stop('physics_addtend')
+      call mpas_timer_stop('physics_get_tend')
 #endif
 
       !
@@ -594,29 +594,6 @@ subroutine atm_srk3(domain, dt, itimestep)
             end do
             call mpas_timer_stop('atm_compute_dyn_tend')
 
-#ifdef DO_PHYSICS
-!            call mpas_timer_start('physics_addtend')
-!            block => domain % blocklist
-!            do while (associated(block))
-!               call mpas_pool_get_subpool(block % structs, 'mesh', mesh)
-!               call mpas_pool_get_subpool(block % structs, 'state', state)
-!               call mpas_pool_get_subpool(block % structs, 'diag', diag)
-!               call mpas_pool_get_subpool(block % structs, 'tend', tend)
-!               call mpas_pool_get_subpool(block % structs, 'tend_physics', tend_physics)
-!               call physics_addtend( block, &
-!                                      mesh, &
-!                                     state, &     
-!                                      diag, &
-!                                      tend, &
-!                              tend_physics, &
-!                           block % configs, &
-!                                   rk_step, &
-!                          dynamics_substep  )
-!               block => block % next
-!            end do
-!            call mpas_timer_stop('physics_addtend')
-#endif
-
 
             !***********************************
             !  need tendencies at all edges of owned cells -
@@ -5508,6 +5485,7 @@ subroutine atm_init_coupled_diagnostics(state, time_lev, diag, mesh, configs, &
       real (kind=RKIND), dimension(:,:), pointer :: u
       real (kind=RKIND), dimension(:,:), pointer :: w
       real (kind=RKIND), dimension(:,:), pointer :: pressure_p
+      real (kind=RKIND), dimension(:,:), pointer :: pressure_base
       real (kind=RKIND), dimension(:,:), pointer :: exner
       real (kind=RKIND), dimension(:,:), pointer :: exner_base
       real (kind=RKIND), dimension(:), pointer :: fzm, fzp
@@ -5540,6 +5518,7 @@ subroutine atm_init_coupled_diagnostics(state, time_lev, diag, mesh, configs, &
       call mpas_pool_get_array(state, 'u', u, time_lev)
       call mpas_pool_get_array(state, 'w', w, time_lev)
       call mpas_pool_get_array(diag, 'pressure_p', pressure_p)
+      call mpas_pool_get_array(diag, 'pressure_base', pressure_base)
       call mpas_pool_get_array(diag, 'exner', exner)
       call mpas_pool_get_array(diag, 'exner_base', exner_base)
       call mpas_pool_get_array(mesh, 'fzm', fzm)
@@ -5620,6 +5599,7 @@ subroutine atm_init_coupled_diagnostics(state, time_lev, diag, mesh, configs, &
       do iCell=cellStart,cellEnd
          do k=1,nVertLevels
             exner(k,iCell) = (zz(k,iCell) * (rgas/p0) * (rtheta_p(k,iCell) + rtheta_base(k,iCell)))**rcv
+            exner_base(k,iCell) = (zz(k,iCell) * (rgas/p0) * (rtheta_base(k,iCell)))**rcv  ! WCS addition 20180403
          end do
       end do
 
@@ -5629,6 +5609,7 @@ subroutine atm_init_coupled_diagnostics(state, time_lev, diag, mesh, configs, &
                                                * (  exner(k,iCell) * rtheta_p(k,iCell) &
                                                   + rtheta_base(k,iCell) * (exner(k,iCell) - exner_base(k,iCell)) &
                                                  )
+            pressure_base(k,iCell) = zz(k,iCell) * rgas * exner_base(k,iCell) * rtheta_base(k,iCell)      ! WCS addition 20180403
          end do
       end do
 

src/core_atmosphere/mpas_atm_core.F

@@ -45,6 +45,7 @@ function atm_core_init(domain, startTimeStamp) result(ierr)
       type (mpas_pool_type), pointer :: diag
       type (field2DReal), pointer :: u_field, pv_edge_field, ru_field, rw_field
       character (len=StrKIND), pointer :: xtime
+      character (len=StrKIND), pointer :: initial_time1, initial_time2
       type (MPAS_Time_Type) :: startTime
 
       integer, pointer :: nVertLevels, maxEdges, maxEdges2, num_scalars
@@ -153,6 +154,13 @@ function atm_core_init(domain, startTimeStamp) result(ierr)
          call mpas_pool_get_array(state, 'xtime', xtime, 1)
          xtime = startTimeStamp
 
+         ! Initialize initial_time in second time level. We need to do this because initial state
+         ! is read into time level 1, and if we write output from the set of state arrays that
+         ! represent the original time level 2, the initial_time field will be invalid.
+         call mpas_pool_get_array(state, 'initial_time', initial_time1, 1)
+         call mpas_pool_get_array(state, 'initial_time', initial_time2, 2)
+         initial_time2 = initial_time1
+
          block => block % next
       end do