Merge branch 'release-v6.0'

This merge introduces v6.0 of all MPAS models. * release-v6.0: (2051 commits) Reimplement C++ support in ESM Makefiles Minor edits to Steve's Registry updates Updates/corrections to Registry descriptions and units Minor edits to formatting in registry Change '%i' to '$i' in call to mpas_log_write from mpas_block_decomp_cells_for_proc Edits to variable descriptions in Registry files More updates to Registry file descriptions Updates to Registry descriptions Change default for config_nvertlevels from 41 to 55 for MPAS-Atmosphere Fix incorrect size of 'hlanduse' array in GWDO field computation Reorganizes Registry.xml for ocean users guide Updates to Registry to get User's Guide to build Update version number to 6.0 Remove mpas_threading.o dependency on mpas_log.o Compute initial w field in bit-reproducible way Remove exner_base, pressure_base from IC file, compute these during start up Remove 'soilcat_bot' field from init_atmosphere core Minimize the size of atmosphere IC files with no change to model results Change time series stats restart name format Change time series stats output name format ...
MPAS-Dev · Apr 17, 2018 · ece5f71 · ece5f71
2 parents 7221fbd + 105aa0a
commit ece5f71
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-MPAS-v5.3
+MPAS-v6.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for

diff --git a/src/Makefile.in.ACME b/src/Makefile.in.ACME
@@ -13,7 +13,7 @@ else
 endif
 # End duplicated logic
 
-include $(CASEROOT)/Macros
+include $(CASEROOT)/Macros.make
 
 ifneq ($(wildcard core_$(CORE)/build_options.mk), ) # Check for build_options.mk
     include core_$(CORE)/build_options.mk
@@ -27,7 +27,7 @@ ifeq "$(CORE)" "ocean"
     COMPONENT=ocn
 else ifeq "$(CORE)" "landice"
     COMPONENT=glc
-else ifeq "$(CORE)" "cice"
+else ifeq "$(CORE)" "seaice"
     COMPONENT=ice
 endif
 
@@ -44,14 +44,14 @@ CC=$(MPICC)
 CXX=$(MPICXX)
 NETCDF=$(NETCDF_PATH)
 PNETCDF=$(PNETCDF_PATH)
-PIO=$(EXEROOT)/pio
+PIO=$(INSTALL_SHAREDPATH)/pio
 FILE_OFFSET = -DOFFSET64BIT
 override CFLAGS += -DMPAS_NO_LOG_REDIRECT -DMPAS_NO_ESMF_INIT -DMPAS_ESM_SHR_CONST -DMPAS_PERF_MOD_TIMERS
 override FFLAGS += -DMPAS_NO_LOG_REDIRECT -DMPAS_NO_ESMF_INIT -DMPAS_ESM_SHR_CONST -DMPAS_PERF_MOD_TIMERS
 override CPPFLAGS += $(CPPDEFS) $(MODEL_FORMULATION) $(FILE_OFFSET) $(ZOLTAN_DEFINE) -DMPAS_NO_LOG_REDIRECT -DMPAS_NO_ESMF_INIT -DMPAS_ESM_SHR_CONST -D_MPI -DMPAS_NAMELIST_SUFFIX=$(NAMELIST_SUFFIX) -DMPAS_EXE_NAME=$(EXE_NAME) -DMPAS_PERF_MOD_TIMERS
-override CPPINCLUDES += -I$(EXEROOT)/$(COMPONENT)/source/inc -I$(SHAREDPATH)/include -I$(SHAREDPATH)/$(COMP_INTERFACE)/$(ESMFDIR)/$(NINST_VALUE)/csm_share -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
-override FCINCLUDES += -I$(EXEROOT)/$(COMPONENT)/source/inc -I$(SHAREDPATH)/include -I$(SHAREDPATH)/$(COMP_INTERFACE)/$(ESMFDIR)/$(NINST_VALUE)/csm_share -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
-LIBS += -L$(PIO) -L$(PNETCDF)/lib -L$(NETCDF)/lib -L$(LIBROOT) -L$(SHAREDPATH)/lib -lpio -lpnetcdf -lnetcdf
+override CPPINCLUDES += -I$(EXEROOT)/$(COMPONENT)/source/inc -I$(INSTALL_SHAREDPATH)/include -I$(INSTALL_SHAREDPATH)/$(COMP_INTERFACE)/$(ESMFDIR)/$(NINST_VALUE)/csm_share -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
+override FCINCLUDES += -I$(EXEROOT)/$(COMPONENT)/source/inc -I$(INSTALL_SHAREDPATH)/include -I$(INSTALL_SHAREDPATH)/$(COMP_INTERFACE)/$(ESMFDIR)/$(NINST_VALUE)/csm_share -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
+LIBS += -L$(PIO) -L$(PNETCDF)/lib -L$(NETCDF)/lib -L$(LIBROOT) -L$(INSTALL_SHAREDPATH)/lib -lpio -lpnetcdf -lnetcdf
 
 ifneq (,$(findstring FORTRANUNDERSCORE, $(CPPFLAGS)))
 ifeq (,$(findstring DUNDERSCORE, $(CPPFLAGS)))

diff --git a/src/Makefile.in.CESM b/src/Makefile.in.CESM
@@ -13,7 +13,7 @@ else
 endif
 # End duplicated logic
 
-include $(CASEROOT)/Macros
+include $(CASEROOT)/Macros.make
 
 ifneq ($(wildcard core_$(CORE)/build_options.mk), ) # Check for build_options.mk
     include core_$(CORE)/build_options.mk
@@ -27,7 +27,7 @@ ifeq "$(CORE)" "ocean"
     COMPONENT=ocn
 else ifeq "$(CORE)" "landice"
     COMPONENT=glc
-else ifeq "$(CORE)" "cice"
+else ifeq "$(CORE)" "seaice"
     COMPONENT=ice
 endif
 

diff --git a/src/core_atmosphere/Makefile b/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:
 

diff --git a/src/core_atmosphere/Registry.xml b/src/core_atmosphere/Registry.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="5.3">
+<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"/>
@@ -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"/>

diff --git a/src/core_atmosphere/diagnostics/convective_diagnostics.F b/src/core_atmosphere/diagnostics/convective_diagnostics.F
@@ -7,8 +7,9 @@
 !
 module convective_diagnostics
 
-    use mpas_derived_types, only : MPAS_pool_type, MPAS_clock_type
+    use mpas_derived_types, only : MPAS_pool_type, MPAS_clock_type, MPAS_LOG_ERR, MPAS_LOG_CRIT
     use mpas_kind_types, only : RKIND
+    use mpas_log, only : mpas_log_write
 
     type (MPAS_pool_type), pointer :: mesh
     type (MPAS_pool_type), pointer :: state
@@ -748,7 +749,7 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
         endif
       enddo
     ENDIF
-    if(debug_level.ge.100) print *,'  kmax,maxthe = ',kmax,maxthe
+    if(debug_level.ge.100) call mpas_log_write('  kmax,maxthe = $i $r', intArgs=(/kmax/), realArgs=(/maxthe/))
 
   ELSEIF(source.eq.3)THEN
     ! use mixed layer
@@ -775,13 +776,12 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
       avgth = 0.0
       avgqv = 0.0
       k = 2
-      if(debug_level.ge.100) print *,'  ml_depth = ',ml_depth
-      if(debug_level.ge.100) print *,'  k,z,th,q:'
-      if(debug_level.ge.100) print *,1,z(1),th(1),q(1)
+      if(debug_level.ge.100) call mpas_log_write('  ml_depth = $r', realArgs=(/ml_depth/))
+      if(debug_level.ge.100) call mpas_log_write('  k,z,th,q: $i $r $r $r', intArgs=(/1/), realArgs=(/z(1),th(1),q(1)/))
 
       do while( (z(k).le.ml_depth) .and. (k.le.nk) )
 
-        if(debug_level.ge.100) print *,k,z(k),th(k),q(k)
+        if(debug_level.ge.100) call mpas_log_write('$i $r $r $r', intArgs=(/k/), realArgs=(/z(k),th(k),q(k)/))
 
         avgth = avgth + 0.5*(z(k)-z(k-1))*(th(k)+th(k-1))
         avgqv = avgqv + 0.5*(z(k)-z(k-1))*(q(k)+q(k-1))
@@ -793,12 +793,12 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
       th2 = th(k-1)+(th(k)-th(k-1))*(ml_depth-z(k-1))/(z(k)-z(k-1))
       qv2 =  q(k-1)+( q(k)- q(k-1))*(ml_depth-z(k-1))/(z(k)-z(k-1))
 
-      if(debug_level.ge.100) print *,999,ml_depth,th2,qv2
+      if(debug_level.ge.100) call mpas_log_write('999 $r $r $r', realArgs=(/ml_depth,th2,qv2/))
 
       avgth = avgth + 0.5*(ml_depth-z(k-1))*(th2+th(k-1))
       avgqv = avgqv + 0.5*(ml_depth-z(k-1))*(qv2+q(k-1))
 
-      if(debug_level.ge.100) print *,k,z(k),th(k),q(k)
+      if(debug_level.ge.100) call mpas_log_write('$i $r $r $r', intArgs=(/k/), realArgs=(/z(k),th(k),q(k)/))
 
       avgth = avgth/ml_depth
       avgqv = avgqv/ml_depth
@@ -807,17 +807,16 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
 
     ENDIF
 
-    if(debug_level.ge.100) print *,avgth,avgqv
+    if(debug_level.ge.100) call mpas_log_write('$r $r', realArgs=real((/avgth,avgqv/),kind=RKIND))
 
   ELSE
 
-!    print *
-!    print *,'  Unknown value for source'
-!    print *
-!    print *,'  source = ',source
-!    print *
-!    stop
-    write(0,*) 'getcape: unknown value for source'
+!    call mpas_log_write('')
+!    call mpas_log_write('  Unknown value for source')
+!    call mpas_log_write('')
+!    call mpas_log_write('  source = $i', intArgs=(/source/))
+!    call mpas_log_write('', messageType=MPAS_LOG_CRIT)
+    call mpas_log_write('getcape: unknown value for source', messageType=MPAS_LOG_ERR)
     return
 
   ENDIF
@@ -862,13 +861,13 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
     endif
 
       the = getthe(p2,t2,t2,qv2)
-      if(debug_level.ge.100) print *,'  the = ',the
+      if(debug_level.ge.100) call mpas_log_write('  the = $r', realArgs=(/the/))
 
 !---- begin ascent of parcel ----!
 
       if(debug_level.ge.100)then
-        print *,'  Start loop:'
-        print *,'  p2,th2,qv2 = ',p2,th2,qv2
+        call mpas_log_write('  Start loop:')
+        call mpas_log_write('  p2,th2,qv2 = $r $r $r', realArgs=(/p2,th2,qv2/))
       endif
 
     do while( doit .and. (k.lt.nk) )
@@ -932,16 +931,16 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
                        +lhs*(qi2-qi1)/(cpm*tbar)     &
                        +(rm/cpm-rd/cp)*alog(p2/p1) )
 
-          if(i .gt. 90 .and. debug_level .gt. 0) print *,i,th2,thlast,th2-thlast
+          if(i .gt. 90 .and. debug_level .gt. 0) call mpas_log_write('$i $r $r $r', intArgs=(/i/), realArgs=(/th2,thlast,th2-thlast/))
           if(i .gt. 100)then
-!            print *
-!            print *,'  Error:  lack of convergence'
-!            print *
-!            print *,'  ... stopping iteration '
-!            print *
+!            call mpas_log_write('')
+!            call mpas_log_write('  Error:  lack of convergence')
+!            call mpas_log_write('')
+!            call mpas_log_write('  ... stopping iteration ')
+!            call mpas_log_write('')
 !            stop 1001
             if (debug_level .gt. 0) then
-               write(0,*) 'getcape: lack of convergence'
+               call mpas_log_write('getcape: lack of convergence', messageType=MPAS_LOG_ERR)
             end if
             return
           endif
@@ -963,11 +962,11 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
           ql2 = 0.0
           qi2 = 0.0
         ELSEIF(adiabat.le.0.or.adiabat.ge.5)THEN
-!          print *
-!          print *,'  Undefined adiabat'
-!          print *
+!          call mpas_log_write('')
+!          call mpas_log_write('  Undefined adiabat')
+!          call mpas_log_write('')
 !          stop 10000
-          write(0,*) 'getcape: Undefined adiabat'
+          call mpas_log_write('getcape: Undefined adiabat', messageType=MPAS_LOG_ERR)
           return
         ENDIF
 
@@ -988,11 +987,11 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
         parea =  0.5*b2*dz*frac
         narea = narea-0.5*b1*dz*(1.0-frac)
         if(debug_level.ge.200)then
-          print *,'      b1,b2 = ',b1,b2
-          print *,'      p1,ps,p2 = ',p(k-1),ps,p(k)
-          print *,'      frac = ',frac
-          print *,'      parea = ',parea
-          print *,'      narea = ',narea
+          call mpas_log_write('      b1,b2 = $r $r', realArgs=(/b1,b2/))
+          call mpas_log_write('      p1,ps,p2 = $r $r $r', realArgs=(/p(k-1),ps,p(k)/))
+          call mpas_log_write('      frac = $r', realArgs=(/frac/))
+          call mpas_log_write('      parea = $r', realArgs=(/parea/))
+          call mpas_log_write('      narea = $r', realArgs=(/narea/))
         endif
         cin  = cin  + narea
         narea = 0.0
@@ -1003,11 +1002,11 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
         parea =  0.5*b1*dz*frac
         narea = -0.5*b2*dz*(1.0-frac)
         if(debug_level.ge.200)then
-          print *,'      b1,b2 = ',b1,b2
-          print *,'      p1,ps,p2 = ',p(k-1),ps,p(k)
-          print *,'      frac = ',frac
-          print *,'      parea = ',parea
-          print *,'      narea = ',narea
+          call mpas_log_write('      b1,b2 = $r $r', realArgs=(/b1,b2/))
+          call mpas_log_write('      p1,ps,p2 = $r $r $r', realArgs=(/p(k-1),ps,p(k)/))
+          call mpas_log_write('      frac = $r', realArgs=(/frac/))
+          call mpas_log_write('      parea = $r', realArgs=(/parea/))
+          call mpas_log_write('      narea = $r', realArgs=(/narea/))
         endif
       elseif( b2.lt.0.0 )then
         ! still collecting negative buoyancy
@@ -1022,8 +1021,7 @@ subroutine getcape( nk , p_in , t_in , td_in, cape , cin )
       cape = cape + max(0.0,parea)
 
       if(debug_level.ge.200)then
-        write(6,102) p2,b1,b2,cape,cin,cloud
-102     format(5(f13.4),2x,l1)
+        call mpas_log_write('$r $r $r $r $r $l', realArgs=(/p2,b1,b2,cape,cin/), logicArgs=(/cloud/))
       endif
 
       if( (p(k).le.10000.0).and.(b2.lt.0.0) )then