Update MPAS dynamical core to version 8.4.0

.gitmodules

@@ -14,7 +14,7 @@
         path          = src/dynamics/mpas/dycore
         url           = https://github.com/MPAS-Dev/MPAS-Model.git
         fxsparse      = ../.mpas_sparse_checkout
-        fxtag         = v8.3.1
+        fxtag         = v8.4.0
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 [submodule "ncar-physics"]

src/dynamics/mpas/assets/0001-Fix-Fortran-standard-violation.patch

@@ -0,0 +1,45 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Kuan-Chih Wang <kuanchihw@ucar.edu>
+Date: Tue, 21 Apr 2026 13:50:09 -0600
+Subject: [PATCH] Fix Fortran standard violation due to pointer argument not
+ being associated
+
+At line 1970, if the `DO_PHYSICS` macro is undefined, the `diag_physics` pointer
+will not be initialized by the call to `mpas_pool_get_subpool`, and therefore
+its pointer association status will remain undefined.
+
+However, at line 2250, this pointer is used as an argument to call `atm_compute_dyn_tend`,
+which constitutes a Fortran standard violation.
+
+Quoted from Fortran 2023,
+
+> 15.5.2.4 Argument association
+> Except in references to intrinsic inquiry functions, a pointer actual argument that
+> corresponds to a nonoptional nonpointer dummy argument shall be pointer associated with
+> a target.
+
+This bug can lead to a runtime crash for models that use MPAS as a dynamical core
+(e.g., CAM, CAM-SIMA).
+
+Fix this issue by adding the `pointer` attribute to the `diag_physics` dummy argument
+for the `atm_compute_dyn_tend` subroutine.
+---
+ src/core_atmosphere/dynamics/mpas_atm_time_integration.F | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+index 238ca7235..c16072976 100644
+--- a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
++++ b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+@@ -5813,7 +5813,7 @@ module atm_time_integration
+       type (mpas_pool_type), intent(in) :: state
+       type (mpas_pool_type), intent(in) :: diag
+       type (mpas_pool_type), intent(in) :: mesh
+-      type (mpas_pool_type), intent(in) :: diag_physics
++      type (mpas_pool_type), pointer, intent(in) :: diag_physics
+       type (mpas_pool_type), intent(in) :: configs
+       integer, intent(in) :: nVertLevels              ! for allocating stack variables
+       integer, intent(in) :: rk_step, dynamics_substep
+-- 
+2.48.1
+

src/dynamics/mpas/assets/0002-Add-missing-argument-intent.patch

@@ -0,0 +1,28 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Kuan-Chih Wang <kuanchihw@ucar.edu>
+Date: Tue, 21 Apr 2026 14:35:05 -0600
+Subject: [PATCH] Add missing argument intent
+
+Throughout the `atm_compute_dyn_tend` subroutine, the `tend_physics` pointer
+never changes its pointer association status. Add the missing `intent(in)`
+attribute for better safety.
+---
+ src/core_atmosphere/dynamics/mpas_atm_time_integration.F | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+index c16072976..b6e620fe1 100644
+--- a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
++++ b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+@@ -5809,7 +5809,7 @@ module atm_time_integration
+       ! Dummy arguments
+       !
+       type (mpas_pool_type), intent(inout) :: tend
+-      type (mpas_pool_type), pointer :: tend_physics
++      type (mpas_pool_type), pointer, intent(in) :: tend_physics
+       type (mpas_pool_type), intent(in) :: state
+       type (mpas_pool_type), intent(in) :: diag
+       type (mpas_pool_type), intent(in) :: mesh
+-- 
+2.48.1
+

src/dynamics/mpas/assets/0003-Avoid-implicit-save-attribute.patch

@@ -0,0 +1,29 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Kuan-Chih Wang <kuanchihw@ucar.edu>
+Date: Tue, 21 Apr 2026 14:49:58 -0600
+Subject: [PATCH] Avoid implicit `save` attribute during variable declaration
+
+In Fortran, explicit initialization of a variable implies the `save` attribute,
+which may have surprising result and is not thread-safe.
+
+Avoid doing it to conform to the Fortran best practices.
+---
+ src/core_atmosphere/dynamics/mpas_atm_time_integration.F | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+index b6e620fe1..227fbde86 100644
+--- a/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
++++ b/src/core_atmosphere/dynamics/mpas_atm_time_integration.F
+@@ -1918,7 +1918,7 @@ module atm_time_integration
+       type (mpas_pool_type), pointer :: diag_physics
+       type (mpas_pool_type), pointer :: mesh
+       type (mpas_pool_type), pointer :: tend
+-      type (mpas_pool_type), pointer :: tend_physics => null()
++      type (mpas_pool_type), pointer :: tend_physics
+       type (mpas_pool_type), pointer :: lbc  ! regional_MPAS addition
+
+       real (kind=RKIND), dimension(:,:), pointer :: w
+-- 
+2.48.1
+

src/dynamics/mpas/assets/Makefile.in.CESM

@@ -37,7 +37,7 @@ export BUILD_TARGET    := N/A
 export CORE            := atmosphere
 export EXE_NAME        := atmosphere_model
 export GEN_F90         := false
-export GIT_VERSION     := $(shell git -C "$(MPAS_SRC_ROOT)" describe --always --dirty --tags || echo "N/A")
+export GIT_VERSION     := $(shell git -C "$(MPAS_SRC_ROOT)" describe --always --dirty --tags 2>/dev/null || echo "N/A")
 export NAMELIST_SUFFIX := atmosphere
 
 # Customize variables (e.g., build options) for use with CESM.
@@ -101,7 +101,7 @@ libmpas-prepare: libmpas-apply-patch libmpas-archiver-script.txt libmpas-preview
 .PHONY: libmpas-apply-patch
 libmpas-apply-patch:
 	@for file in *.patch; do \
-		if git apply --check -p2 "$${file}"; then \
+		if [ -f "$${file}" ] && git apply --check -p2 "$${file}" 1>/dev/null 2>&1; then \
 			echo "Applying $${file}"; \
 			git apply -p2 "$${file}"; \
 		fi; \

src/dynamics/mpas/assets/generate_namelist_definition.py

@@ -5,6 +5,7 @@
 '''
 
 import argparse
+import re
 import textwrap
 import xml.etree.ElementTree as ET
 
@@ -14,6 +15,7 @@
     'assimilation',
     'iau',
     'limited_area',
+    'musica',
     'physics',
     'restart'
 ]
@@ -101,7 +103,7 @@ def parse_argument() -> argparse.Namespace:
         default=None,
         type=str,
         required=False,
-        help='XML schema for CAM-SIMA namelist definition file.',
+        help='XML schema (i.e., entry_id_pg.xsd) for CAM-SIMA namelist definition file.',
         dest='nml_xsd'
     )
 
@@ -193,13 +195,21 @@ def translate_element_tree(reg_xml_et: ET.ElementTree) -> ET.ElementTree:
             group_element.text = transform_name(namelist_group.attrib['name'].strip().lower())
 
             # The `type` element.
+            # The `units` element.
             # The `values` element and its containing `value` element.
             type_text = namelist_option.attrib['type'].strip().lower()
+            if 'units' in namelist_option.attrib and namelist_option.attrib['units'].strip() not in ('', '-'):
+                # Filter out illegal characters in accordance with the `entry_id_pg.xsd` XML schema.
+                units_text = re.sub('[^-+A-Za-z0-9 ]', '', namelist_option.attrib['units'].strip())
+            else:
+                units_text = 'none'
             value_text = namelist_option.attrib['default_value']
 
             # Do some sanitization.
             if type_text.startswith('ch'):
                 type_text = 'char*256'
+                # The units of a Fortran character variable is customarily 'none' in accordance with the ESM Standard Names.
+                units_text = 'none'
                 value_text = value_text.strip()
 
                 if not value_text.isascii():
@@ -209,6 +219,8 @@ def translate_element_tree(reg_xml_et: ET.ElementTree) -> ET.ElementTree:
                 value_text = canonicalize_int(value_text)
             elif type_text.startswith('lo'):
                 type_text = 'logical'
+                # The units of a Fortran logical variable is customarily 'flag' in accordance with the ESM Standard Names.
+                units_text = 'flag'
                 value_text = value_text.strip().lower()
 
                 if value_text.startswith(('t', '.t')):
@@ -226,6 +238,9 @@ def translate_element_tree(reg_xml_et: ET.ElementTree) -> ET.ElementTree:
             type_element = ET.SubElement(entry_element, 'type')
             type_element.text = type_text
 
+            units_element = ET.SubElement(entry_element, 'units')
+            units_element.text = units_text
+
             values_element = ET.SubElement(entry_element, 'values')
 
             if entry_element.attrib['id'] in OVERRIDDEN_NAMELIST_OPTION: