Merge branch 'release-v5.0'

This merge introduces v5.0 of all MPAS models.

* release-v5.0: (964 commits)
  Fix issue with 'dzs' when running r8 model with r4 initial conditions
  This merge fixes a restartability error in the new Tiedtke scheme.
  Avoid bit-reproducibility errors in GWDO scheme due to 'kpblmin' and 'kpblmax' computation
  Fix incorrect assignment of 'xlamdd', 'frh', and 'mentrd_rate' in Grell-Freitas scheme
  * In ./src/core_atmosphere/Registry.xml, corrected typo (description instead of   decription) in the definition of the variable nr.
  * In ./src/core_atmosphere/physics/mpas_atmphys_control.F, modified inquiring   about the Thompson microphysics tables in the subroutine physics_table_init.   The modified logic now allows the different tables to be read for each MPI   task.
  * In ./src/core_atmosphere/physics/physics_wrf/module_mp_thompson.F, in subroutine mp_gt_driver,   moved the initialization of variables Nt_c and mu_c before initialization of local mixing ratios   and number concentrations. This change allows a proper initialization of the local variable nc   when is_aerosol_aware is false.
  Add exit messages at the end of core_finalize routines
  Update "possible_values" for physics schemes
  * In ./src/core_atmosphere/physics/mpas_atmphys_control.F, modified checking the   config_gwdo_scheme option to allow bl_ysu_gwdo to be run when the MYNN pbl and   surface layer options are chosen.
  Fix bug in storage and application of IAU tendency contributions
  Update to physics suites: New Tiedtke and YSU GWDO
  Change suite name 'convection_scale_aware' to 'convection_permitting'
  Simplify IAU calls from atm_srk3( )
  Rename 'zz_rtheta_pp_old' to 'rtheta_pp_old'
  Fix bug in location of call to get IAU tendency contributions
  Remove unused variable 'rtheta_pp_old' from atmosphere Registry.xml file
  Final corrections to namelist and variable attributes for MPAS-Atmosphere v5.0
  Initialize t_oml_200m_initial field when climatological OML depth is used
  Add lower bound of 1.0e-8 to vapor pressure in dewpoint calculation
  ...

Author: mgduda

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+The title above should be a 1 line short summary of the issue.
+
+Enter a description of the issue.
+This should include what the symptoms are, and steps to reproduce.
+
+Additionally please enter this information if applicable:
+ - Compiler and version
+ - MPI implementation and version
+ - NetCDF version
+ - Parallel NetCDF version
+ - Parallel IO version
+ - Output of `uname -a`
+ - The make line used to build the executable
+ - The line used to run the executable
+ - Test case used

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,10 @@
+The title above should be a 1 line short summary of the pull request (i.e. what the project the PR represents is intended to do).
+
+Enter a description of this PR. This should include why this PR was created, and what it does.
+
+Testing and relations to other Pull Requests should be added as subsequent comments.
+
+See the below examples for more information.
+https://github.com/MPAS-Dev/MPAS/pull/930
+https://github.com/MPAS-Dev/MPAS/pull/931
+

.gitignore

@@ -18,17 +18,22 @@ src/operators/*.f90
 
 # Executables
 *_model
+build_tables
 
 # NetCDF Files
 *.nc
 
+# Restart timestamp file
+restart_timestamp
+
 # Graph files and partition files
 *.info
 *.info.part.*
 
-# Error and Output log files
+# Error, Output, and Abort log files
 *.out
 *.err
+*.abort
 
 # Text files (For statistical output from ocean model)
 *.txt

INSTALL

@@ -0,0 +1,59 @@
+Installing MPAS
+====
+
+For general information on how to install MPAS, see https://mpas-dev.github.io.
+Additional notes on building MPAS on specific architectures are summarized here.
+
+
+gfortran-clang: Compiling MPAS on MacOSX (10.11 El Capitan - 10.12 Sierra)
+----------
+MPAS should compile out of the box on MacOSX with the standard (OS) clang compiler
+and the gfortran compiler. The gfortran compiler can be installed using homebrew
+(http://brew.sh), or using pre-compiled binaries from the MacOSX HPC website
+(http://hpc.soureforge.net), or it can be compiled by the user from the GNU sources.
+
+The standard clang compiler does not support OpenMP. Users wanting to compile MPAS
+with OpenMP support on MacOSX will have to install the LLVM clang compiler, which is
+accomplished easiest with homebrew. Since this alternative clang compiler is not in
+the standard search/library path, the user will have to modify the call to the clang
+and clang++ executable and add the library path to the compiler flags. Example:
+
+...
+	"FC_PARALLEL = mpif90" \
+	"CC_PARALLEL = mpicc -cc=clang" \
+	"CXX_PARALLEL = mpicxx -cxx=clang++" \
+	"FC_SERIAL = gfortran" \
+	"CC_SERIAL = clang" \
+	"CXX_SERIAL = clang++" \
+	"FFLAGS_PROMOTION = -fdefault-real-8 -fdefault-double-8" \
+	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
+	"CFLAGS_OPT = -O3 -m64" \
+	"CXXFLAGS_OPT = -O3 -m64" \
+	"LDFLAGS_OPT = -O3 -m64" \
+	"FFLAGS_DEBUG = -g -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow" \
+	"CFLAGS_DEBUG = -g -m64" \
+	"CXXFLAGS_DEBUG = -O3 -m64" \
+	"LDFLAGS_DEBUG = -g -m64" \
+...
+
+would become
+
+...
+	"FC_PARALLEL = mpif90" \
+	"CC_PARALLEL = mpicc -cc=/usr/local/opt/llvm/bin/clang" \
+	"CXX_PARALLEL = mpicxx -cxx=/usr/local/opt/llvm/bin/clang++" \
+	"FC_SERIAL = gfortran" \
+	"CC_SERIAL = /usr/local/opt/llvm/bin/clang" \
+	"CXX_SERIAL = /usr/local/opt/llvm/bin/clang++" \
+	"FFLAGS_PROMOTION = -fdefault-real-8 -fdefault-double-8" \
+	"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form -L/usr/local/opt/llvm/lib" \
+	"CFLAGS_OPT = -O3 -m64 -L/usr/local/opt/llvm/lib" \
+	"CXXFLAGS_OPT = -O3 -m64 -L/usr/local/opt/llvm/lib" \
+	"LDFLAGS_OPT = -O3 -m64 -L/usr/local/opt/llvm/lib" \
+	"FFLAGS_DEBUG = -g -m64 -L/usr/local/opt/llvm/lib -ffree-line-length-none -fconvert=big-endian -ffree-form -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow" \
+	"CFLAGS_DEBUG = -g -m64 -L/usr/local/opt/llvm/lib" \
+	"CXXFLAGS_DEBUG = -O3 -m64 -L/usr/local/opt/llvm/lib" \
+	"LDFLAGS_DEBUG = -g -m64 -L/usr/local/opt/llvm/lib" \
+...
+
+assuming that the LLVM clang compiler is installed in /usr/local/opt/llvm.