MICM Chemistry Solver Integration

[K20shores]

This is an issue that tracks this PR on our project board

[dwfncar]

Progress update — 2026-04-18

Reviewer feedback from @mgduda on PR #1425 addressed in two commits on musica_micm_integration:

7a15848d — Address PR MPAS-Dev#1425 review feedback

• core_atmosphere/Registry.xml: moved qAB/qA/qB to end of scalars and tend_qAB/tend_qA/tend_qB to end of scalars_tend, both with array_group="chem_test".
• core_init_atmosphere/Registry.xml: same reorg for symmetry.
• mpas_atm_chemistry.F: removed redundant module-level use mpas_kind_types; RKIND now imported inside chemistry_step where it's actually used.
• mpas_musica.F: wired INITIAL_CONCENTRATION_PROPERTY through micm%get_species_property_double() so MICM species are initialized from the YAML __initial concentration field. init_ab/init_a/init_b placeholders replaced with a single reused initial_profile(:). assign_rate_parameters now called after the species loop so USER_DEFINED reactions have a defined rate.

752f8959 — Propagate MICM solver failures as errors (unsolicited, flagged to mgduda)

• musica_step now sets error_code=1 + descriptive error_message and returns on (a) non-Converged solver state or (b) final_time < time_step. Previously these only emitted log warnings. chemistry_step already routes non-zero error_code through MPAS_LOG_CRIT, so the model now aborts on silent MICM failures rather than advancing with stale state.
• log_solver_stats now fires before the checks so stats leading to a failure are always in the log.

PR body updated with the full abba.yaml contents (mechanism: AB ⇌ A + B via two USER_DEFINED reactions with scaling factors 2e-3 forward, 1e-3 reverse).

Smoke test

Built on Ubuntu/Pop!_OS with the conda-forge mpas env (gfortran / openmpi / netcdf / pnetcdf) and MUSICA=true, using CheMPAS's scripts/check_build_env.sh preflight. Linked against MUSICA-Fortran 0.14.5 / MICM 3.11.0. Ran the supercell idealized case with config_micm_file='abba.yaml', 30 s simulated time, 8 MPI ranks. Results:

Species	t=0 (YAML init)	t=3 s	t=6 s
AB	1.0	0.994018	0.988072
A	0.0	0.005982	0.011921
B	0.0	0.005982	0.011921

Atom conservation [X] + [AB] = 1.0 holds exactly for X ∈ {A, B}. Solver: 9 steps, 9 accepted / 0 rejected, final_time = 3.0 s matches config_dt. Zero model errors.

Status

• Address mgduda's 6 review comments (Registry group, RKIND move, unused decls)
• Answer mgduda's ABBA-config question (YAML in PR body)
• Wire initial concentrations from YAML (bonus; side effect of MPAS MUSICA MICM Solver #5/MPAS MICM State Coupling #6 fix)
• Harden solver failure propagation (bonus; flagged for reviewer)
• Reply on all review threads; re-review requested from mgduda
• Awaiting re-review

Scope note / next PR

This PR still calls MICM with number_of_grid_cells = nVertLevels — i.e. a single column; no MPAS scalars ↔ MICM state%concentrations copy. CheMPAS has the full nCells * nVertLevels coupling (chemistry_to_MICM / MICM_to_chemistry), resolve_mpas_indices, state_ref for advection diagnostics, and photolysis field wiring. Proposal is to keep PR MPAS-Dev#1425 at "solver wiring" scope (which is what the title says and the reviewer accepted) and open a focused follow-up PR for MPAS tracer-state coupling, ported from CheMPAS.