Merge branch 'hotfix-v8.2.2'

This merge addresses several issues in the MPAS-Atmosphere model and in the MPAS
infrastructure. Specific changes in this merge include:

* Fix to a portability issue in the MPAS registry 'parse' tool, which caused
  files in the src/core_<CORE>/inc directory to not be generated correctly at
  build time on some systems (PR #1229).

* Addition of two fields, brtemp and cldmask, that are needed by MPAS-JEDI.
  Although not needed by stand-alone MPAS-Atmosphere, these fields are
  associated with the 'jedi_da' package and therefore have no effect when
  MPAS-Atmosphere is run without setting config_jedi_da = true (PR #1232).

* Removal of a redundant query of the nCellsSolve dimension in the
  physics_run_init routine. The extra query had no impact on results, and its
  removal can be considered clean-up (PR #1236).

Author: mgduda

README.md

@@ -1,4 +1,4 @@
-MPAS-v8.2.1
+MPAS-v8.2.2
 ====
 
 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="8.2.1">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="8.2.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->
@@ -1841,6 +1841,15 @@
                 <var name="surface_pressure" type="real" dimensions="nCells Time" units="Pa"
                      description="Diagnosed surface pressure"/>
 
+                <!-- observation-related variables interfacing to Non-Variational SAtellite-based Cloud Analysis (SACA)  -->
+                <var name="cldmask" type="real" dimensions="nCells Time" units="unitless"
+                     description="cloud mask (1=cloudy ; 0=clear)"
+                     packages="jedi_da"/>
+
+                <var name="brtemp" type="real" dimensions="nCells Time" units="K"
+                     description="brightness temperature to calculate cloud top height; usually from geostationary IR window channel"
+                     packages="jedi_da"/>
+
         </var_struct>
 
         <var_struct name="tend" time_levs="1">

src/core_atmosphere/physics/mpas_atmphys_manager.F

@@ -447,7 +447,6 @@ subroutine physics_run_init(configs,mesh,state,clock,stream_manager)
  call mpas_pool_get_dimension(mesh,'nAerLevels' ,nAerLevels )
  call mpas_pool_get_dimension(mesh,'nOznLevels' ,nOznLevels )
  call mpas_pool_get_dimension(mesh,'nCellsSolve',nCellsSolve)
- call mpas_pool_get_dimension(mesh,'nCellsSolve',nCellsSolve)
  call mpas_pool_get_dimension(mesh,'nSoilLevels',nSoilLevels)
  call mpas_pool_get_dimension(mesh,'nVertLevels',nVertLevels)
 

src/core_init_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="8.2.1">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="8.2.2">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="8.2.1">
+<registry model="mpas" core="landice" core_abbrev="li" version="8.2.2">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="8.2.1">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="8.2.2">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_seaice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="seaice" core_abbrev="seaice" version="8.2.1">
+<registry model="mpas" core="seaice" core_abbrev="seaice" version="8.2.2">
 
 	<dims>
 		<dim name="nCells"

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="8.2.1">
+<registry model="mpas" core="sw" core_abbrev="sw" version="8.2.2">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/core_test/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="test" core_abbrev="test" version="8.2.1">
+<registry model="mpas" core="test" core_abbrev="test" version="8.2.2">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/tools/registry/utility.c

@@ -309,21 +309,26 @@ int parse_macros(void(*callback)(const char *macro, const char *val, va_list ap)
 
 	for (i = 0; i < count; i++) {
 		char *tmp;
-		char *macrotmp;
-		char *macro;
-		char *val;
+		char *saveptr;
+		const char *macro;
+		const char *val;
+		const char *empty = "";
 
 		tmp = strdup(macros[i]);
-		macrotmp = strtok_r(tmp, "=", &val);
 
-		if (macrotmp == NULL || val == NULL) {
+		macro = strtok_r(tmp, "=", &saveptr);
+		val = strtok_r(NULL, "=", &saveptr);
+
+		if (macro == NULL) {
 			return 1;
 		}
 
-		if (strstr(macrotmp, "-D") == macrotmp) {
-			macro = &macrotmp[2];
-		} else {
-			macro = macrotmp;
+		if (val == NULL) {
+			val = empty;
+		}
+
+		if (strstr(macro, "-D") == macro) {
+			macro = &macro[2];
 		}
 
 		if (callback != NULL) {