Merge branch 'hotfix-v5.1'

This merge introduces fixes for MPAS-Atmosphere

* hotfix-v5.1: (24 commits)
  Note in description of config_len_disp that it is also used by 3-d div damping
  Introduce a new, scale-aware 3-d divergence damping scheme for acoustic modes
  Introduced scaling of the gravity-wave absorbing layer coefficient
  Comment-out code in MYNN surface-layer scheme to bound 2-m theta
  Initialize horizontal fluxes for ghost-cell faces in monotonic transport
  Use 'config_extrap_airtemp' to control vertical extrapolation of temperature
  Add check for lapse-rate extrapolation above first-guess data in vertical_interp
  Add namelist option config_extrap_airtemp for extrapolation above/below first-guess levels
  Ensure that temperature is computed if MSLP is needed in isobaric_diagnostics
  Remove .tmp.f90 files from esmf_time_f90 directory when 'make clean' is run
  Replace angle brackets with quotes in include statements in esmf_time_f90
  Change name of preprocessed Fortran files from .f90 to .tmp.f90 in esmf_time_f90
  Provide compatibility with ECMWF 100-289 cm soil layer
  * In ./src/core_atmosphere/physics/mpas_atmphys_driver_radiation_lw.F and   mpas_atmphys_driver_radiation_sw.F, revised the initialization of the   variables re_cloud, re_ice, re_snow, and rre_cloud, rre_ice, and rre_snow,   when config_microp_scheme is set to off.
  Tiny formatting corrections in mpas_init_atm_cases.F
  Bug fix to re-enable the read and interpolation of pressure levels as output by calc_ecmpwf_p.exe from WPS
  Updated INSTALL documentation with known problems on IBM Bluegene and Mac OSX
  Changes to real/double conversion as requested in amendment of 2423776, however 0.0d0_RKIND does not work, need to use 0.0_RKIND
  Removed CPP directives -DSINGLE_PRECISION from Fortran compiler flags as this breaks builds on systems where GEN_F90 is required (e.g. Bluegene)
  Avoid setting invalid pointers to scalar constituents in mpas_atmphys_interface module
  ...

Author: mgduda

INSTALL

@@ -12,7 +12,11 @@ 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
+Caveats:
+
+(1) MPAS cannot be compiled with gfortran-clang if GEN_F90=true.
+
+(2) 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
@@ -57,3 +61,10 @@ would become
 ...
 
 assuming that the LLVM clang compiler is installed in /usr/local/opt/llvm.
+
+
+bluegene: Compiling MPAS on IBM Bluegene using the xl compilers
+----------
+All MPAS cores except the ocean compile on IBM Bluegene using the xl compilers. The ocean
+core currently does not work on IBM Bluegene. Known limitations: OPENMP must be disabled
+(OPENMP=false) for compiling, since the xl compilers do not support nested OpenMP directives.

Makefile

@@ -509,7 +509,6 @@ ifeq "$(OPENMP)" "true"
 endif #OPENMP IF
 
 ifeq "$(PRECISION)" "single"
-	FFLAGS += "-DSINGLE_PRECISION"
 	CFLAGS += "-DSINGLE_PRECISION"
 	CXXFLAGS += "-DSINGLE_PRECISION"
 	override CPPFLAGS += "-DSINGLE_PRECISION"

README.md

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

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="5.0">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="5.1">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -141,7 +141,7 @@
 
                 <nml_option name="config_len_disp" type="real" default_value="120000.0"
                      units="m"
-                     description="Horizontal length scale for Smagorinsky formulation of horizontal diffusion"
+                     description="Horizontal length scale, used by the Smagorinsky formulation of horizontal diffusion and by 3-d divergence damping"
                      possible_values="Positive real values"/>
 
                 <nml_option name="config_visc4_2dsmag" type="real" default_value="0.05"
@@ -224,16 +224,11 @@
                      description="Off-centering parameter for the vertically implicit acoustic integration"
                      possible_values="Positive real values"/>
 
-                <nml_option name="config_smdiv" type="real" default_value="0.025"
+                <nml_option name="config_smdiv" type="real" default_value="0.1"
                      units="-"
                      description="3-d divergence damping coefficient"
                      possible_values="Positive real values"/>
 
-                <nml_option name="config_smdiv_p_forward" type="real" default_value="0.1"
-                     units="-"
-                     description="Fractional forward weighting of the pressure during the acoustic step --- a form of 3D divergence damping"
-                     possible_values="Real values typically in the range 0 to 0.2"/>
-
                 <nml_option name="config_apvm_upwinding" type="real" default_value="0.5" in_defaults="false"
                      units="-"
                      description="Amount of upwinding in APVM"
@@ -1588,9 +1583,6 @@
                 <var name="rho_p_save" type="real" dimensions="nVertLevels nCells Time" units="kg m^{-3}"
                      description="predicted value rho_p, saved before acoustic steps"/>
 
-                <var name="divergence_3d" type="real" dimensions="nVertLevels nCells Time" units="kg m^{-3} s^{-1}"
-                     description="3D divergence used for acoustic filtering"/>
-
                 <var name="kdiff" type="real" dimensions="nVertLevels nCells Time" units="m^2 s^{-1}"
                      description="Smagorinsky horizontal eddy viscosity"/>
 

src/core_atmosphere/diagnostics/isobaric_diagnostics.F

@@ -553,7 +553,7 @@ subroutine interp_diagnostics(mesh, state, time_lev, diag)
            enddo
         enddo
 
-        if (NEED_TEMP .or. NEED_RELHUM .or. NEED_DEWPOINT) then
+        if (NEED_TEMP .or. NEED_RELHUM .or. NEED_DEWPOINT .or. need_mslp) then
            !calculation of temperature at cell centers:
             do iCell = 1,nCells
             do k = 1,nVertLevels