From 54a90a1fd86b245b76e0903c23a3990eb91f1764 Mon Sep 17 00:00:00 2001
From: David Fillmore <fillmore@ucar.edu>
Date: Mon, 10 Nov 2025 10:12:29 -0700
Subject: [PATCH] MICM configuration is now driven by a MUSICA namelist option
 with added logging.

Registry.xml: Added a MUSICA namelist record gated by MPAS_USE_MUSICA with the
`config_micm_file` option so the MICM JSON path can be provided through the
standard configuration system.
mpas_atm_chemistry.F: Removed the hardcoded `chapman.json`, pull the MICM file
path from the configs pool, then propagate errors from `musica_init` via
`mpas_log_write` to fail when initialization breaks.
mpas_musica.F: Track the species description pointer and log each MICM species
name from `state%species_ordering` so users can verify the runtime mapping.
---
 src/core_atmosphere/Registry.xml              |  9 ++++++++
 .../chemistry/mpas_atm_chemistry.F            | 22 ++++++++++---------
 .../chemistry/musica/mpas_musica.F            |  9 +++++++-
 3 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/src/core_atmosphere/Registry.xml b/src/core_atmosphere/Registry.xml
index 4281c40bba..88c0b0928d 100644
--- a/src/core_atmosphere/Registry.xml
+++ b/src/core_atmosphere/Registry.xml
@@ -394,6 +394,15 @@
                      possible_values="`mpas_dmpar', `mpas_halo'"/>
         </nml_record>
 
+#ifdef MPAS_USE_MUSICA
+        <nml_record name="musica" in_defaults="true">
+                <nml_option name="config_micm_file" type="character" default_value=""
+                     units="-"
+                     description="MICM configuration file name"
+                     possible_values="Any valid filename"/>
+        </nml_record>
+#endif
+
 <!-- **************************************************************************************** -->
 <!-- **************************************  Packages  ************************************** -->
 <!-- **************************************************************************************** -->
diff --git a/src/core_atmosphere/chemistry/mpas_atm_chemistry.F b/src/core_atmosphere/chemistry/mpas_atm_chemistry.F
index 39715cf37a..3997cc363f 100644
--- a/src/core_atmosphere/chemistry/mpas_atm_chemistry.F
+++ b/src/core_atmosphere/chemistry/mpas_atm_chemistry.F
@@ -43,7 +43,7 @@ subroutine chemistry_init(configs, dimensions)
         use mpas_musica, only: musica_init
 #endif
         use mpas_log, only : mpas_log_write
-        use mpas_derived_types, only: mpas_pool_type
+        use mpas_derived_types
         use mpas_kind_types, only: StrKIND
         use mpas_pool_routines, only: mpas_pool_get_config, mpas_pool_get_dimension 
 
@@ -51,13 +51,11 @@ subroutine chemistry_init(configs, dimensions)
         type (mpas_pool_type), intent(in) :: dimensions
 
 #ifdef MPAS_USE_MUSICA
-        integer                       :: error_code
-        character(len=:), allocatable :: error_message
-        integer                       :: nVertLevels
-        integer, pointer              :: nVertLevels_ptr
-        ! MUSICA will get the MICM JSON config from a namelist
-        ! hardcode filepath for now
-        character(len=StrKIND) :: filepath = 'chapman.json'
+        character(len=StrKIND), pointer :: filepath_ptr
+        integer                         :: error_code
+        character(len=:), allocatable   :: error_message
+        integer                         :: nVertLevels
+        integer, pointer                :: nVertLevels_ptr
 #endif
 
         call mpas_log_write('Initializing chemistry packages...')
@@ -66,9 +64,13 @@ subroutine chemistry_init(configs, dimensions)
         call mpas_pool_get_dimension(dimensions, 'nVertLevels', nVertLevels_ptr)
         nVertLevels = nVertLevels_ptr
 
-        call musica_init(filepath, nVertLevels, error_code, error_message)
+        call mpas_pool_get_config(configs, 'config_micm_file', filepath_ptr)
 
-        ! TODO check error_code and generate MPAS error log message
+        call musica_init(filepath_ptr, nVertLevels, error_code, error_message)
+
+        if (error_code /= 0) then
+            call mpas_log_write(error_message, messageType=MPAS_LOG_CRIT)
+        end if
 #endif
 
     end subroutine chemistry_init
diff --git a/src/core_atmosphere/chemistry/musica/mpas_musica.F b/src/core_atmosphere/chemistry/musica/mpas_musica.F
index 649b2b3624..0f4ef8cd45 100644
--- a/src/core_atmosphere/chemistry/musica/mpas_musica.F
+++ b/src/core_atmosphere/chemistry/musica/mpas_musica.F
@@ -61,9 +61,10 @@ subroutine musica_init(filename_of_micm_configuration, &
 
         type(error_t)  :: error
         type(string_t) :: micm_version
-
+        type(string_t) :: description
         ! TEMPORARY: Hard-coded options for the MICM solver
         integer :: solver_type = RosenbrockStandardOrder
+        integer :: i_species
 
         micm_version = get_micm_version()
 
@@ -77,6 +78,12 @@ subroutine musica_init(filename_of_micm_configuration, &
         state => micm%get_state(number_of_grid_cells, error)
         if (has_error_occurred(error, error_message, error_code)) return
 
+        associate(map => state%species_ordering)
+            do i_species = 1, map%size( )
+                call mpas_log_write('MICM species: ' // map%name(i_species))
+            end do
+        end associate
+
     end subroutine musica_init
 
     !------------------------------------------------------------------------