Merge branch 'release-v3.0'

This merge introduces v3.0 of all MPAS models.

* release-v3.0: (346 commits)
  When writing restart_timestamp file, trim the time stamp variable.
  Use constant extrapolation below the surface for RH.
  Place upper-bound on saturation vapor pressure to avoid negative densities in MPAS-A initialization, particularly near the model top.
  Change vertical grid stretching exponent from 1.8 to 1.5 for Jablonowski and Williamson test case.
  Initialize intent(out) argument 'ierr' in mpas_core_setup_clock() for init_atmosphere core.
  Move mpas_atm_advection model from core_atmosphere to core_init_atmosphere.
  Adding a trim when writing restart_timestamp
  Add units to enstrophy
  Updating interval division to use linear
  Removing un-needed latex equations from units in global stats.
  Edit GM Registry descriptions.
  Change to cap: Restart_timestamp
  Halt if I/O errors (other than clobber errors) are encountered in MPAS-Atmosphere.
  Add code to write 'restart_timestamp' file for atmosphere core.
  Restore restart_timestamp file, add "forcing"
  LI Registry cleanup for 3.0
  Change a few default namelist flags
  Fixing an issue with an improperly formatted read statement
  Remove some unneeded trim statments from timers
  Fixing formating of warning messages for missing namelist records
  ...

.gitignore

@@ -1,6 +1,7 @@
 # Ignore Files in the MPAS Direcory
 
 # All pre-processed Fortran files in MPAS specific directories
+src/core_*/Registry_processed.xml
 src/core_*/*.f90
 src/framework/*.f90
 src/driver/*.f90
@@ -44,3 +45,12 @@ src/registry/parse
 
 # Ignore MPAS core build files.
 .mpas_core_*
+
+# Ignore all runtime config files
+namelist.*
+streams.*
+stream_list.*
+
+# Intermediate files that may be produced by Intel compilers
+*.i
+*.i90

Makefile

@@ -1,5 +1,4 @@
-#MODEL_FORMULATION = -DNCAR_FORMULATION
-MODEL_FORMULATION = -DLANL_FORMULATION
+MODEL_FORMULATION = 
 
 
 dummy:
@@ -36,6 +35,20 @@ ftn:
 	"USE_PAPI = $(USE_PAPI)" \
 	"CPPFLAGS = $(MODEL_FORMULATION) -D_MPI -DUNDERSCORE" )
 
+titan-cray:
+	( $(MAKE) all \
+	"FC_PARALLEL = ftn" \
+	"CC_PARALLEL = cc" \
+	"FC_SERIAL = ftn" \
+	"CC_SERIAL = gcc" \
+	"FFLAGS_OPT = -s integer32 -default64 -O3 -f free -N 255 -em -ef" \
+	"CFLAGS_OPT = -O3" \
+	"LDFLAGS_OPT = -O3" \
+	"CORE = $(CORE)" \
+	"DEBUG = $(DEBUG)" \
+	"USE_PAPI = $(USE_PAPI)" \
+	"CPPFLAGS = $(MODEL_FORMULATION) -D_MPI -DUNDERSCORE" )
+
 pgi:
 	( $(MAKE) all \
 	"FC_PARALLEL = mpif90" \
@@ -108,7 +121,7 @@ ifort-gcc:
 	"CFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"FFLAGS_DEBUG = -real-size 64 -g -convert big_endian -FR -CU -CB -check all -fpe0 -traceback" \
-	"CFLAGS_DEBUG = -g -traceback" \
+	"CFLAGS_DEBUG = -g" \
 	"LDFLAGS_DEBUG = -g -fpe0 -traceback" \
 	"CORE = $(CORE)" \
 	"DEBUG = $(DEBUG)" \
@@ -197,7 +210,7 @@ intel-nersc:
 	"CC_PARALLEL = cc" \
 	"FC_SERIAL = ftn" \
 	"CC_SERIAL = cc" \
-	"FFLAGS_OPT = -real-size 64 -O3 -FR" \
+	"FFLAGS_OPT = -real-size 64 -O3 -convert big_endian -FR" \
 	"CFLAGS_OPT = -O3" \
 	"LDFLAGS_OPT = -O3" \
 	"CORE = $(CORE)" \
@@ -226,29 +239,57 @@ CPPINCLUDES =
 FCINCLUDES = 
 LIBS = 
 ifneq ($(wildcard $(PIO)/lib), ) # Check for newer PIO version
-	CPPINCLUDES = -I$(NETCDF)/include -I$(PIO)/include -I$(PNETCDF)/include
-	FCINCLUDES = -I$(NETCDF)/include -I$(PIO)/include -I$(PNETCDF)/include
-	LIBS = -L$(PIO)/lib -L$(PNETCDF)/lib -L$(NETCDF)/lib -lpio -lpnetcdf
+	CPPINCLUDES = -I$(PIO)/include
+	FCINCLUDES = -I$(PIO)/include
+	LIBS = -L$(PIO)/lib -lpio
 else
-	CPPINCLUDES = -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
-	FCINCLUDES = -I$(NETCDF)/include -I$(PIO) -I$(PNETCDF)/include
-	LIBS = -L$(PIO) -L$(PNETCDF)/lib -L$(NETCDF)/lib -lpio -lpnetcdf
+	CPPINCLUDES = -I$(PIO)
+	FCINCLUDES = -I$(PIO)
+	LIBS = -L$(PIO) -lpio
 endif
 
-NCLIB = -lnetcdf
-NCLIBF = -lnetcdff
-ifneq ($(wildcard $(NETCDF)/lib/libnetcdff.*), ) # CHECK FOR NETCDF4
-	LIBS += $(NCLIBF)
-endif # CHECK FOR NETCDF4
-LIBS += $(NCLIB)
+ifneq "$(PNETCDF)" ""
+	CPPINCLUDES += -I$(PNETCDF)/include
+	FCINCLUDES += -I$(PNETCDF)/include
+	LIBS += -L$(PNETCDF)/lib -lpnetcdf
+endif
+
+ifneq "$(NETCDF)" ""
+	CPPINCLUDES += -I$(NETCDF)/include
+	FCINCLUDES += -I$(NETCDF)/include
+	LIBS += -L$(NETCDF)/lib
+	NCLIB = -lnetcdf
+	NCLIBF = -lnetcdff
+	ifneq ($(wildcard $(NETCDF)/lib/libnetcdff.*), ) # CHECK FOR NETCDF4
+		LIBS += $(NCLIBF)
+	endif # CHECK FOR NETCDF4
+	LIBS += $(NCLIB)
+endif
 
 RM = rm -f
 CPP = cpp -P -traditional
 RANLIB = ranlib
 
-
 ifdef CORE
 
+ifneq ($(wildcard src/core_$(CORE)), ) # CHECK FOR EXISTENCE OF CORE DIRECTORY
+
+ifneq ($(wildcard src/core_$(CORE)/build_options.mk), ) # Check for build_options.mk
+include src/core_$(CORE)/build_options.mk
+else # ELSE Use Default Options
+EXE_NAME=$(CORE)_model
+NAMELIST_SUFFIX=$(CORE)
+endif
+
+override CPPFLAGS += -DMPAS_NAMELIST_SUFFIX=$(NAMELIST_SUFFIX)
+override CPPFLAGS += -DMPAS_EXE_NAME=$(EXE_NAME)
+
+else # ELSE CORE DIRECTORY CHECK
+
+report_builds: all
+
+endif # END CORE DIRECTORY CHECK
+
 ifeq "$(DEBUG)" "true"
 
 ifndef FFLAGS_DEBUG
@@ -302,7 +343,6 @@ else
 	GEN_F90_MESSAGE="MPAS was built with .F files."
 endif
 
-
 ifneq ($(wildcard .mpas_core_*), ) # CHECK FOR BUILT CORE
 
 ifneq ($(wildcard .mpas_core_$(CORE)), ) # CHECK FOR SAME CORE AS ATTEMPTED BUILD.
@@ -326,10 +366,32 @@ else
 	CONTINUE=true
 endif # END IF BUILT CORE CHECK
 
+ifneq ($(wildcard namelist.$(NAMELIST_SUFFIX)), ) # Check for generated namelist file.
+	NAMELIST_MESSAGE="A default namelist file (namelist.$(NAMELIST_SUFFIX).defaults) has been generated, but namelist.$(NAMELIST_SUFFIX) has not been modified."
+else
+	NAMELIST_MESSAGE="A default namelist file (namelist.$(NAMELIST_SUFFIX).defaults) has been generated and copied to namelist.$(NAMELIST_SUFFIX)."
+endif
+
+ifneq ($(wildcard streams.$(NAMELIST_SUFFIX)), ) # Check for generated streams file.
+	STREAM_MESSAGE="A default streams file (streams.$(NAMELIST_SUFFIX).defaults) has been generated, but streams.$(NAMELIST_SUFFIX) has not been modified."
+else
+	STREAM_MESSAGE="A default streams file (streams.$(NAMELIST_SUFFIX).defaults) has been generated and copied to streams.$(NAMELIST_SUFFIX)."
+endif
+
+
 ifeq "$(findstring clean, $(MAKECMDGOALS))" "clean" # CHECK FOR CLEAN TARGET
 	override AUTOCLEAN=false
 endif # END OF CLEAN TARGET CHECK
 
+VER=$(shell git describe --dirty 2> /dev/null)
+#override CPPFLAGS += -DMPAS_GIT_VERSION=$(VER)
+
+ifeq "$(findstring v, $(VER))" "v"
+	override CPPFLAGS += -DMPAS_GIT_VERSION=$(VER)
+else
+	override CPPFLAGS += -DMPAS_GIT_VERSION="unknown"
+endif # END OF GIT DESCRIBE VERSION
+
 ####################################################
 # Section for adding external libraries and includes
 ####################################################
@@ -348,6 +410,11 @@ all: core_error
 
 else
 
+ifeq ($(wildcard src/core_$(CORE)/build_options.mk), ) # Check for build_options.mk
+report_builds:
+	@echo "CORE=$(CORE)"
+endif
+
 ifeq "$(CONTINUE)" "true"
 all: mpas_main
 else
@@ -356,7 +423,8 @@ endif
 
 endif
 
-mpas_main: 
+
+mpas_main:
 ifeq "$(AUTOCLEAN)" "true"
 	$(RM) .mpas_core_*
 endif
@@ -376,10 +444,17 @@ endif
                  FCINCLUDES="$(FCINCLUDES)" \
                  CORE="$(CORE)"\
                  AUTOCLEAN="$(AUTOCLEAN)" \
-                 GEN_F90="$(GEN_F90)"
-	@echo "$(CORE)" > .mpas_core_$(CORE)
-	if [ -e src/$(CORE)_model ]; then mv src/$(CORE)_model .; fi
-	@echo ""
+                 GEN_F90="$(GEN_F90)" \
+                 NAMELIST_SUFFIX="$(NAMELIST_SUFFIX)" \
+                 EXE_NAME="$(EXE_NAME)"
+
+	@echo "$(EXE_NAME)" > .mpas_core_$(CORE)
+	if [ -e src/$(EXE_NAME) ]; then mv src/$(EXE_NAME) .; fi
+	if [ -e src/inc/namelist.$(NAMELIST_SUFFIX).defaults ]; then mv src/inc/namelist.$(NAMELIST_SUFFIX).defaults .; fi
+	if [ ! -e namelist.$(NAMELIST_SUFFIX) ]; then cp namelist.$(NAMELIST_SUFFIX).defaults namelist.$(NAMELIST_SUFFIX); fi
+	if [ -e src/inc/streams.$(NAMELIST_SUFFIX).defaults ]; then mv src/inc/streams.$(NAMELIST_SUFFIX).defaults .; fi
+	if [ ! -e streams.$(NAMELIST_SUFFIX) ]; then cp streams.$(NAMELIST_SUFFIX).defaults streams.$(NAMELIST_SUFFIX); fi
+	for f in `find src/inc -name "stream_list.*"`; do mv $$f .; done
 	@echo "*******************************************************************************"
 	@echo $(DEBUG_MESSAGE)
 	@echo $(PARALLEL_MESSAGE)
@@ -389,11 +464,15 @@ ifeq "$(AUTOCLEAN)" "true"
 	@echo $(AUTOCLEAN_MESSAGE)
 endif
 	@echo $(GEN_F90_MESSAGE)
+	@echo $(NAMELIST_MESSAGE)
+	@echo $(STREAM_MESSAGE)
 	@echo "*******************************************************************************"
 clean:
-	$(RM) .mpas_core_*
 	cd src; $(MAKE) clean RM="$(RM)" CORE="$(CORE)"
-	$(RM) $(CORE)_model
+	$(RM) .mpas_core_*
+	$(RM) $(EXE_NAME)
+	$(RM) namelist.$(NAMELIST_SUFFIX).defaults
+	$(RM) streams.$(NAMELIST_SUFFIX).defaults
 core_error:
 	@echo ""
 	@echo "*******************************************************************************"

README.md

@@ -1,4 +1,4 @@
-MPAS-v2.1
+MPAS-v3.0
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for