CAM Codon Formula Status Map

Curated formula/process view generated from the current routines table at 2026-06-01T19:24:15+00:00.

done
done-native-island
processing
partial
none
unknown
missing mapping → unknown
3Formula sections
21Formula terms
68Mapped routines4699 LOC, deduplicated
30Not done / active routines0 missing refs
2done formula terms35 routines · 2599 LOC
1done-native-island formula terms3 routines · 334 LOC
0processing formula terms0 routines · 0 LOC
18partial formula terms30 routines · 1766 LOC
0none formula terms0 routines · 0 LOC
0unknown formula terms0 routines · 0 LOC
How to read this page: equations and routine mappings are curated documentation, while routine statuses are read from the live database. A formula term is marked complete only when its required mapped routines are complete. Manual status overrides automatic status, exactly as on the main dashboard.

1. SE dynamical core primitive equations

Hydrostatic spectral-element dycore terms. The formulas are curated summaries; the live status comes from the mapped routines in the current dashboard database.

done: 0 done-native-island: 0 processing: 0 partial: 7 none: 0 unknown: 0

Horizontal momentum

Updates horizontal wind from pressure/geopotential gradients, kinetic energy, vorticity coupling, and physics momentum tendencies.

partial
∂v/∂t = −∇φ − ∇K + ζ × v − ρ−1∇p + Fv

Mapped LOC for this formula term: 144

• A formula is only complete when both the RHS assembly and its SE operators are complete.

compute_and_apply_rhs
partial
RHS assembly
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 106 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; compute_and_apply_rhs remains native dycore RHS with derivative calls, physics thermodynamics, DSS pack/exchange/unpack, and optional diagnostics; no validated same-routine Codon body.
gradient_sphere
done
gradient operator
src/dynamics/se/share/derivative_mod.F90 · subroutine · 15 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
vorticity_sphere
done
vorticity operator
src/dynamics/se/share/derivative_mod.F90 · subroutine · 18 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
applycamforcing_dynamics
done
physics forcing
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 5 LOC
Evidence: file_touched_since_start=true
Manual note: agent w08 partial200; commit d11003b; job 6318030.desched1; selector APPLYCAMFORCING_DYNAMICS_IMPL=codon; proof atm.log line 5173 applycamforcing_dynamics implementation = codon; compare_6318030 overall_numeric_equal=True; guard validate-run passed

Thermodynamic energy

Advects temperature, applies compressional heating through omega, and adds physics temperature tendencies.

partial
∂T/∂t = −v·∇T + κTω/p + FT

Mapped LOC for this formula term: 149

compute_and_apply_rhs
partial
thermodynamic RHS
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 106 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; compute_and_apply_rhs remains native dycore RHS with derivative calls, physics thermodynamics, DSS pack/exchange/unpack, and optional diagnostics; no validated same-routine Codon body.
gradient_sphere
done
temperature gradient
src/dynamics/se/share/derivative_mod.F90 · subroutine · 15 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
applycamforcing_dynamics
done
FT forcing
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 5 LOC
Evidence: file_touched_since_start=true
Manual note: agent w08 partial200; commit d11003b; job 6318030.desched1; selector APPLYCAMFORCING_DYNAMICS_IMPL=codon; proof atm.log line 5173 applycamforcing_dynamics implementation = codon; compare_6318030 overall_numeric_equal=True; guard validate-run passed
preq_omega_ps
partial
omega/pressure diagnostic
src/dynamics/se/share/prim_si_mod.F90 · subroutine · 23 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.

Continuity / layer mass

Conserves dry/full layer pressure thickness through horizontal mass flux divergence.

partial
∂dp/∂t = −∇·(v·dp)

Mapped LOC for this formula term: 125

compute_and_apply_rhs
partial
dp3d update
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 106 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; compute_and_apply_rhs remains native dycore RHS with derivative calls, physics thermodynamics, DSS pack/exchange/unpack, and optional diagnostics; no validated same-routine Codon body.
divergence_sphere
done
mass divergence
src/dynamics/se/share/derivative_mod.F90 · subroutine · 18 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
prim_advance_exp
partial
RK stage driver
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 1 LOC
Evidence: file_touched_since_start=true
Manual note: parallel partial35 integrated main d7474d3 fail-closed: no same-routine proof in integrated fixed case; native dycore orchestration remains

Hydrostatic pressure / geopotential

Builds pressure, Exner, virtual temperature, and geopotential terms used by the RHS.

partial
φ(k) = φs + Σ RdTv ln(pk+1/2/pk−1/2)

Mapped LOC for this formula term: 121

compute_and_apply_rhs
partial
inline hydrostatic terms
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 106 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; compute_and_apply_rhs remains native dycore RHS with derivative calls, physics thermodynamics, DSS pack/exchange/unpack, and optional diagnostics; no validated same-routine Codon body.
gradient_sphere
done
pressure/geopotential gradient
src/dynamics/se/share/derivative_mod.F90 · subroutine · 15 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done

Tracer transport and vertical remap

Advects tracer mass, applies limiter/remap logic, and keeps tracer mass consistent with dp.

partial
∂(Q·dp)/∂t = −∇·(Q·v·dp) + FQ·dp

Mapped LOC for this formula term: 225

euler_step
done
tracer RK/euler step
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 126 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
prim_advec_tracers_remap_rk2
partial
tracer remap RK2
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 21 LOC
Evidence: file_touched_since_start=true
Manual note: partial100 closable6 recovery: restored partial after subagent 503/unvalidated lane state; no source commit, no fresh same-routine proof, no overall_numeric_equal=True closure for prim_advec_tracers_remap_rk2
prim_advec_tracers_remap
partial
tracer orchestration
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 4 LOC
Evidence: file_touched_since_start=true
Manual note: agent w08 partial200; left partial: fixed-case default dispatches to large native Prim_Advec_Tracers_remap_rk2 body; helper Codon coverage is not same-routine closure
remap_q_ppm
done
PPM tracer remap
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 44 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
remap1
partial
vertical remap kernel
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 6 LOC
Evidence: file_touched_since_start=true
Manual note: agent w14_dynamics_se_lowloc partial200; left partial: remap1 active body is large native vertical remap with tridiagonal/monotonicity loops and abort/timer control; PPM branch delegates to remap_Q_ppm helper path, not a same-routine closure
vertical_remap
done
vertical remap driver
src/dynamics/se/share/prim_advection_mod.F90 · subroutine · 24 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done

Vertical pressure velocity diagnostic

Computes omega for thermodynamic coupling and tracer transport diagnostics.

partial
ω(k) = ∫(−∇·(v·dp)) dη + v·∇p

Mapped LOC for this formula term: 56

preq_omega_ps
partial
omega diagnostic
src/dynamics/se/share/prim_si_mod.F90 · subroutine · 23 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
divergence_sphere
done
flux divergence
src/dynamics/se/share/derivative_mod.F90 · subroutine · 18 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
gradient_sphere
done
pressure gradient
src/dynamics/se/share/derivative_mod.F90 · subroutine · 15 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done

Hyperviscosity / numerical diffusion

Applies stabilizing diffusion when the selected configuration has nonzero hyperviscosity.

partial
dp ← dp + Δt · ν · ∇⁴(dp)

Mapped LOC for this formula term: 81

advance_hypervis_dp
partial
biharmonic diffusion
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 70 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; advance_hypervis_dp still performs native hyperviscosity loops plus laplace/biharmonic kernels, boundary exchange, and energy-heating updates; no same-routine Codon wrapper/proof.
divergence_sphere_wk
done
work-array divergence
src/dynamics/se/share/derivative_mod.F90 · subroutine · 11 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done

2. SE timestep orchestration and coupling

Runge-Kutta/subcycling control, dycore entry points, and physics-dynamics grid coupling.

done: 0 done-native-island: 0 processing: 0 partial: 4 none: 0 unknown: 0

Ullrich RK / qsplit-rsplit-nsplit control

Coordinates RK stages, time-level updates, and dycore subcycling around the RHS formulas.

partial
un+1 = RK5(un, RHS, Δt; qsplit, rsplit, nsplit)

Mapped LOC for this formula term: 73

prim_step
partial
per-step driver
src/dynamics/se/share/prim_driver_mod.F90 · subroutine · 21 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
prim_run_subcycle
done
subcycle driver
src/dynamics/se/share/prim_driver_mod.F90 · subroutine · 41 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
prim_advance_exp
partial
explicit RK driver
src/dynamics/se/share/prim_advance_mod.F90 · subroutine · 1 LOC
Evidence: file_touched_since_start=true
Manual note: parallel partial35 integrated main d7474d3 fail-closed: no same-routine proof in integrated fixed case; native dycore orchestration remains
dyn_run
partial
dycore entry point
src/dynamics/se/dyn_comp.F90 · subroutine · 10 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.

Physics ↔ dynamics coupling

Maps state and tendencies between the physics grid and the SE GLL dycore grid.

partial
physics grid ⇄ GLL grid: FT, Fv, FQ, T, U, PS

Mapped LOC for this formula term: 207

p_d_coupling
partial
physics to dynamics
src/dynamics/se/dp_coupling.F90 · subroutine · 55 LOC
Evidence: file_touched_since_start=true
Manual note: agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; p_d_coupling remains large native physics-dynamics coupling orchestration with derived state, exchanges, and update loops; no same-routine Codon body/proof.
d_p_coupling
partial
dynamics to physics
src/dynamics/se/dp_coupling.F90 · subroutine · 86 LOC
Evidence: file_touched_since_start=true
Manual note: agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; d_p_coupling still owns native dynamics-physics transposes, pbuf/history/frontogenesis branches, and derived_phys call; no same-routine Codon default-path validation.
stepon_run1
partial
cam_run1 bridge
src/dynamics/se/stepon.F90 · subroutine · 11 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
stepon_run2
partial
cam_run2 bridge
src/dynamics/se/stepon.F90 · subroutine · 49 LOC
Evidence: file_touched_since_start=true
Manual note: agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; stepon_run2 remains large native timestep orchestration across dynamics/physics state, subcycles, timers, and exchanges; no same-routine Codon proof.
stepon_run3
partial
cam_run3 bridge
src/dynamics/se/stepon.F90 · subroutine · 6 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.

CAM run phases and checksum surface

High-level CAM phases that bound physics forcing, dycore execution, restart/history, and checksum visibility.

partial
cam_run1 → cam_run2 → cam_run3(dyn_run) → cam_run4

Mapped LOC for this formula term: 54

cam_run1
partial
physics pre-step
src/control/cam_comp.F90 · subroutine · 13 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
cam_run2
partial
physics→dycore coupling
src/control/cam_comp.F90 · subroutine · 13 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
cam_run3
partial
dycore execution/checksum
src/control/cam_comp.F90 · subroutine · 9 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
cam_run4
partial
restart/history IO
src/control/cam_comp.F90 · subroutine · 19 LOC
Evidence: file_touched_since_start=true
Manual note: fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.

DSS / element boundary exchange

Packs, exchanges, and unpacks element-edge data so SE operators see continuous boundary values.

partial
uglobal = M−1 Σe Meue

Mapped LOC for this formula term: 182

• Long-edge routines are shown as supporting routines and do not alone determine formula completeness.

edgevpack
partial
edge pack
src/dynamics/se/share/edge_mod.F90 · subroutine · 66 LOC
Evidence: file_touched_since_start=true
Manual note: agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; edgevpack still owns native edge packing, reversal, buffer/derived-type mutation, and neighbor/corner logic; no same-routine Codon default body or BFB proof.
edgevunpack
done
edge unpack
src/dynamics/se/share/edge_mod.F90 · subroutine · 29 LOC
Evidence: file_touched_since_start=true
Manual note: agent codex; partial100-loc replenish se_small2; isolated lane /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/replenish_se_small2; commit aebe131578a757185266bbced46706cf58753f43; job 6322743.desched1; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/replenish_se_small2/output/run_se_small2_20260531_123512; selector run_environment.txt.6322743.desched1.260531-123531:257 SE_MISC_HELPERS_IMPL=codon; overall_numeric_equal=True; guard passed receipt .codon_guard_receipts/0e793d38a7d3ebad2328c2249468741b8f8768870f41cce0d4207611bb44a6c2.json; proof atm.log.6322743.desched1.260531-123531.gz:1028 edgevunpack implementation = codon
longedgevpack
partial
long-edge pack · optional
src/dynamics/se/share/edge_mod.F90 · subroutine · 58 LOC
Evidence: file_touched_since_start=true
Manual note: agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; longedgevpack still owns native long-edge packing, reversal and buffer/derived-type mutation; no same-routine Codon default body or fresh BFB proof.
longedgevunpackmin
done
long-edge unpack · optional
src/dynamics/se/share/edge_mod.F90 · subroutine · 29 LOC
Evidence: file_touched_since_start=true
Manual note: agent codex; partial100-loc replenish se_small2; isolated lane /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/replenish_se_small2; commit aebe131578a757185266bbced46706cf58753f43; job 6322743.desched1; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/replenish_se_small2/output/run_se_small2_20260531_123512; selector run_environment.txt.6322743.desched1.260531-123531:257 SE_MISC_HELPERS_IMPL=codon; overall_numeric_equal=True; guard passed receipt .codon_guard_receipts/0e793d38a7d3ebad2328c2249468741b8f8768870f41cce0d4207611bb44a6c2.json; proof atm.log.6322743.desched1.260531-123531.gz:1280 longedgevunpackmin implementation = codon

3. Aerosol and chemistry process formulas

Chemistry/aerosol terms from the same status database. These show how the formula map can cover non-dycore process code without changing the underlying routine status model.

done: 2 done-native-island: 1 processing: 0 partial: 7 none: 0 unknown: 0

Wet deposition / scavenging

Removes aerosol/gas species through in-cloud and below-cloud scavenging pathways.

partial
∂q/∂t|wetdep = −Λrain,cloud · q + source/sink corrections

Mapped LOC for this formula term: 570

washo
done
washout/scavenging
src/chemistry/mozart/mo_neu_wetdep.F90 · subroutine · 396 LOC
Evidence: file_touched_since_start=true
Manual note: agent w03 partial100-loc validated existing HEAD 1a29ff3; no source diff/no new commit; job 6321039.desched1 cpudev; run_dir /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/w03/output/run; proof atm.log.6321039.desched1.260531-030957.gz:8702 washo implementation = codon; :8704 neu_wetdep_washo_columns_codon_wrap entered (washo column dispatcher = codon, dempirical implementation = codon); run_environment WASHO_IMPL=codon WASHO_DEMPIRICAL_IMPL=codon; compare overall_numeric_equal=True
neu_wetdep_tend
partial
wetdep tendency
src/chemistry/mozart/mo_neu_wetdep.F90 · subroutine · 77 LOC
Evidence: file_touched_since_start=true
Manual note: partial100 closable6 recovery: restored partial after subagent 503/unvalidated lane state; no source commit, no fresh same-routine proof, no overall_numeric_equal=True closure for neu_wetdep_tend
wetdepa_v2
done
aerosol wetdep
src/chemistry/aerosol/wetdep.F90 · subroutine · 73 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true
set_srf_wetdep
done
surface wetdep setup
src/chemistry/utils/modal_aero_deposition.F90 · subroutine · 24 LOC
Evidence: file_touched_since_start=true
Manual note: commit d333c7d; direct invoke proof for same-routine set_srf_wetdep; selectors AERO_MODEL_WETDEP_IMPL=native SET_SRF_WETDEP_IMPL=codon; job 6325607.desched1; run /glade/derecho/scratch/ruitong/tmp/icesm_se_ne16_f1850c5_codonimpl_run_20260531_223718_set_srf_wetdep_cpudev/run; atm.log.6325607.desched1.260531-223740.gz:8476 set_srf_wetdep direct = codon; bin_fluxes active; overall_numeric_equal=True

Dry deposition velocity

Computes dry-deposition flux from resistance/velocity parameterizations and applies it to species.

partial
Fdry = vd · C,   vd = (Ra + Rb + Rc)−1

Mapped LOC for this formula term: 689

aero_model_drydep
done
modal aerosol drydep
src/chemistry/modal_aero/aero_model.F90 · subroutine · 242 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
drydep_xactive
partial
gas drydep driver
src/chemistry/mozart/mo_drydep.F90 · subroutine · 227 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; mo_drydep parent/file/PIO/init/orchestration/native child paths remain, so status restored to partial.
dvel_inti_xactive
partial
velocity initialization
src/chemistry/mozart/mo_drydep.F90 · subroutine · 167 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; mo_drydep parent/file/PIO/init/orchestration/native child paths remain, so status restored to partial.
set_srf_drydep
done
surface drydep setup
src/chemistry/utils/modal_aero_deposition.F90 · subroutine · 28 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true
calcram
done
aerodynamic resistance
src/chemistry/aerosol/drydep_mod.F90 · subroutine · 25 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true

Gas-aerosol exchange / uptake

Transfers condensable species between gas and aerosol phases using uptake/equilibrium rates.

done
∂qaer/∂t = kuptake(qgas − qeq)

Mapped LOC for this formula term: 401

modal_aero_gasaerexch_sub
done
exchange kernel
src/chemistry/modal_aero/modal_aero_gasaerexch.F90 · subroutine · 176 LOC
Evidence: file_touched_since_start=true
Manual note: agent w04 partial100-loc validated HEAD 1a29ff33a24b no new source commit; job 6321030.desched1; proof: modal_aero_gasaerexch_sub direct codon entered; overall_numeric_equal=True; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/w04/output/run
modal_aero_gasaerexch_init
done
initialization
src/chemistry/modal_aero/modal_aero_gasaerexch.F90 · subroutine · 80 LOC
Evidence: file_touched_since_start=true
Manual note: agent w03 partial200; commit 9928dd3; job 6316374.desched1; run /glade/derecho/scratch/ruitong/cam_codon_parallel_partial200_20260530/w03/output/run; overall_numeric_equal=True; proof line: modal_aero_gasaerexch_init implementation = codon
aero_model_gasaerexch
done
model driver
src/chemistry/modal_aero/aero_model.F90 · subroutine · 63 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
modal_aero_soaexch
done
SOA exchange
src/chemistry/modal_aero/modal_aero_gasaerexch.F90 · subroutine · 59 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true
gas_aer_uptkrates
done
uptake rates
src/chemistry/modal_aero/modal_aero_gasaerexch.F90 · subroutine · 23 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true

Coagulation transfer

Moves aerosol number and mass between modes through Brownian/coagulation kernels.

partial
∂Ni/∂t = −ΣjKijNiNj + transfer terms

Mapped LOC for this formula term: 304

modal_aero_coag_sub
done
coagulation kernel
src/chemistry/modal_aero/modal_aero_coag.F90 · subroutine · 110 LOC
Evidence: file_touched_since_start=true
Manual note: agent w04 partial100-loc validated HEAD 1a29ff33a24b no new source commit; job 6321030.desched1; proof: modal_aero_coag_sub direct codon entered; overall_numeric_equal=True; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/w04/output/run
getcoags
done-native-island
coagulation coefficients
src/chemistry/modal_aero/modal_aero_coag.F90 · subroutine · 92 LOC
Evidence: file_touched_since_start=true
Manual note: agent w04 partial100-loc validated HEAD 1a29ff33a24b no new source commit; job 6321030.desched1; proof: modal_aero_getcoags_core entered (formula core = codon, correction tables = native Fortran-owned); native island: correction tables/pre-index block remain Fortran-owned; overall_numeric_equal=True; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/w04/output/run
modal_aero_coag_init
done
initialization
src/chemistry/modal_aero/modal_aero_coag.F90 · subroutine · 79 LOC
Evidence: file_touched_since_start=true
Manual note: agent w03 partial200; commit 9928dd3; job 6316374.desched1; run /glade/derecho/scratch/ruitong/cam_codon_parallel_partial200_20260530/w03/output/run; overall_numeric_equal=True; proof line: modal_aero_coag_init implementation = codon
getcoags_wrapper_f
partial
wrapper/glue
src/chemistry/modal_aero/modal_aero_coag.F90 · subroutine · 23 LOC
Evidence: file_touched_since_start=true
Manual note: agent w03 partial140 fail-closed; job 6315850.desched1 BFB pass overall_numeric_equal=True, but no same-routine atm.log proof for this routine; commit ce34ae0/a453bf7 only closes qqcw_set_ptr and qqcw_get_field

New particle / ice nucleation

Creates new aerosol/ice number through parameterized nucleation rates.

done
J = f(T, RH, aerosol, chemistry),   ΔN = J · Δt

Mapped LOC for this formula term: 255

modal_aero_newnuc_sub
done
modal aerosol new nucleation
src/chemistry/modal_aero/modal_aero_newnuc.F90 · subroutine · 109 LOC
Evidence: file_touched_since_start=true
Manual note: agent w04 partial100-loc validated HEAD 1a29ff33a24b no new source commit; job 6321030.desched1; proof: modal_aero_newnuc_sub direct codon entered; overall_numeric_equal=True; run /glade/derecho/scratch/ruitong/cam_codon_partial100_loc_20260531/w04/output/run
nucleate_ice_cam_calc
done
ice nucleation
src/physics/cam/nucleate_ice_cam.F90 · subroutine · 94 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
Manual note: commit 07ad062; job 6294534.desched1 selector NUCLEATE_ICE_CAM_PREP_IMPL=codon; proof nucleate_ice_cam_calc direct = codon modal nucleation loop; qsat/svp/history/outfld native CAM API islands; overall_numeric_equal=True
nucleati
done
ice nucleation kernel
src/physics/cam/nucleate_ice.F90 · subroutine · 52 LOC
Evidence: file_touched_since_start=true
Manual note: commit f899a6c; first physics partial batch; selector NUCLEATI_IMPL=codon; proof nucleati direct = codon scalar ice nucleation kernel; native svp_water/svp_ice callbacks; overall_numeric_equal=True

Photolysis rates

Computes wavelength-integrated photolysis rates modified by clouds, columns, and lookup tables.

partial
Ji = ∫ σi(λ) Φi(λ) F(λ) dλ

Mapped LOC for this formula term: 326

photo_register
partial
registration/setup
src/chemistry/mozart/mo_photo.F90 · subroutine · 158 LOC
Evidence: file_touched_since_start=true
Manual note: coordinator 2026-05-31: integration cleanup 499c0ea dropped unexecuted photo_register attempt; final job 6320670 had no same-routine proof line, remains partial
table_photo
done
lookup table
src/chemistry/mozart/mo_photo.F90 · subroutine · 84 LOC
Evidence: file_touched_since_start=true; preserved_prior_auto_status=done
cloud_mod
done
cloud modifier
src/chemistry/mozart/mo_photo.F90 · subroutine · 36 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true
jlong_photo
done
longwave photolysis
src/chemistry/mozart/mo_jlong.F90 · subroutine · 27 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true
set_ub_col
done
column setup
src/chemistry/mozart/mo_photo.F90 · subroutine · 21 LOC
Evidence: file_touched_since_start=true; same_routine_body_direct_codon_call_scan=true

Gas-phase chemistry driver

Advances gas chemistry source/sink equations and associated initialization state.

partial
dc/dt = P(c, T, J) − L(c, T, J) · c

Mapped LOC for this formula term: 294

gas_phase_chemdr
partial
chemistry driver
src/chemistry/mozart/mo_gas_phase_chemdr.F90 · subroutine · 193 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; existing gas-phase Codon stage helpers do not close the parent/native orchestration, so status restored to partial.
gas_phase_chemdr_inti
partial
initialization
src/chemistry/mozart/mo_gas_phase_chemdr.F90 · subroutine · 101 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; existing gas-phase Codon stage helpers do not close the parent/native orchestration, so status restored to partial.

Surface emissions and unit conversion

Injects surface emissions into chemical/aerosol tracers with time interpolation and mass conversion.

partial
q ← q + Δt · Esurface / massair

Mapped LOC for this formula term: 143

srf_emissions_inti
partial
emission initialization
src/chemistry/mozart/mo_srf_emissions.F90 · subroutine · 67 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem2; fail-closed after job 6322529.desched1: no same-routine done proof in atm.log and/or native orchestration remains; overall_numeric_equal=True for lane but row not closed
set_srf_emissions
partial
emission application
src/chemistry/mozart/mo_srf_emissions.F90 · subroutine · 37 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-loc replenish chem2; fail-closed after job 6322529.desched1: no same-routine done proof in atm.log and/or native orchestration remains; overall_numeric_equal=True for lane but row not closed
aero_model_emissions
done
aerosol model emissions
src/chemistry/modal_aero/aero_model.F90 · subroutine · 24 LOC
Evidence: file_touched_since_start=true
Manual note: partial100-closable6 dashboard cleanup; current main e7d3b99 includes prior aero_model_emissions Codon shell commits; final integration job 6324078.desched1 run /glade/derecho/scratch/ruitong/cam_codon_partial100_closable6_20260531/integration/output/run_integration_partial100_closable6_3rows_20260531_1845; proof "aero_model_emissions implementation = codon" and "aero_model_emissions_codon_wrap entered (parent shell = codon)" plus all-shell stage dispatch; overall_numeric_equal=True; native path is explicit AERO_MODEL_EMISSIONS_IMPL=native fallback, outfld remains CAM API boundary.
chem_emissions
done
chemistry driver
src/chemistry/mozart/chemistry.F90 · subroutine · 15 LOC
Evidence: file_touched_since_start=true
Manual note: worker w04 partial200; existing source wrapper at commit 6485d44; job 6317477; proof chem_emissions implementation = codon plus chem_emissions_codon_wrap entered parent shell = codon; overall_numeric_equal=True; guard validate-run passed

Water uptake and condensate diagnostic

Computes aerosol water uptake / condensate terms where BFB-sensitive native islands may remain.

done-native-island
mwet = mdry + mH2O(RH, κ, Ddry)

Mapped LOC for this formula term: 242

modal_aero_wateruptake_dr
done-native-island
water uptake
src/chemistry/utils/modal_aero_wateruptake.F90 · subroutine · 112 LOC
Evidence: file_touched_since_start=true
Manual note: agent w05 partial100-loc validated 2026-05-31; commit 1a29ff3; job 6321022.desched1; proof atm.log.6321022.desched1.260531-030447.gz:8371-8372 and proof modal_aero_wateruptake_dr.proof; MODAL_AERO_WATERUPTAKE_DR_IMPL=codon run_environment:284; overall_numeric_equal=True; native islands base_pow=native_array, kohler_stage=quartic_sqrt_pow_native, wet_stage=all_codon_pow_native.
instratus_condensate
done-native-island
stratus condensate
src/physics/cam/cldwat2m_macro.F90 · subroutine · 130 LOC
Evidence: file_touched_since_start=true
Manual note: commit d05bb71; first physics partial batch; selector/proof CLDWAT2M_INSTRATUS_CONDENSATE_IMPL=codon / cldwat2m_instratus_condensate direct = codon; native expression callbacks for BFB: qsat_water, astG_single, aist_single; job 6252322.desched1; overall_numeric_equal=True; audit 2026-05-27 reclass done-native-island

Not done / next work

Deduplicated formula-mapped routines whose current display status is none, partial, processing, or unknown.

StatusLOCRoutineFileEvidence / note
partial 227 drydep_xactive src/chemistry/mozart/mo_drydep.F90
file_touched_since_start=true
partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; mo_drydep parent/file/PIO/init/orchestration/native child paths remain, so status restored to partial.
partial 193 gas_phase_chemdr src/chemistry/mozart/mo_gas_phase_chemdr.F90
file_touched_since_start=true
partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; existing gas-phase Codon stage helpers do not close the parent/native orchestration, so status restored to partial.
partial 167 dvel_inti_xactive src/chemistry/mozart/mo_drydep.F90
file_touched_since_start=true
partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; mo_drydep parent/file/PIO/init/orchestration/native child paths remain, so status restored to partial.
partial 158 photo_register src/chemistry/mozart/mo_photo.F90
file_touched_since_start=true
coordinator 2026-05-31: integration cleanup 499c0ea dropped unexecuted photo_register attempt; final job 6320670 had no same-routine proof line, remains partial
partial 106 compute_and_apply_rhs src/dynamics/se/share/prim_advance_mod.F90
file_touched_since_start=true
agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; compute_and_apply_rhs remains native dycore RHS with derivative calls, physics thermodynamics, DSS pack/exchange/unpack, and optional diagnostics; no validated same-routine Codon body.
partial 101 gas_phase_chemdr_inti src/chemistry/mozart/mo_gas_phase_chemdr.F90
file_touched_since_start=true
partial100-loc replenish chem1 fail-closed 2026-05-31: no lane source change or same-routine Codon proof for this row; existing gas-phase Codon stage helpers do not close the parent/native orchestration, so status restored to partial.
partial 86 d_p_coupling src/dynamics/se/dp_coupling.F90
file_touched_since_start=true
agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; d_p_coupling still owns native dynamics-physics transposes, pbuf/history/frontogenesis branches, and derived_phys call; no same-routine Codon default-path validation.
partial 77 neu_wetdep_tend src/chemistry/mozart/mo_neu_wetdep.F90
file_touched_since_start=true
partial100 closable6 recovery: restored partial after subagent 503/unvalidated lane state; no source commit, no fresh same-routine proof, no overall_numeric_equal=True closure for neu_wetdep_tend
partial 70 advance_hypervis_dp src/dynamics/se/share/prim_advance_mod.F90
file_touched_since_start=true
agent w01 partial100-loc fail-closed 2026-05-31: no source change/commit; advance_hypervis_dp still performs native hyperviscosity loops plus laplace/biharmonic kernels, boundary exchange, and energy-heating updates; no same-routine Codon wrapper/proof.
partial 69 modal_aero_calcsize_init src/chemistry/utils/modal_aero_calcsize.F90
file_touched_since_start=true
agent w05 partial100-loc fail-closed 2026-05-31; source inspection shows native phys_getopts, pbuf_set_field, addfld/add_default/history and rename setup in modal_aero_calcsize_init; no same-routine direct Codon selector/proof in job 6321022; stays partial.
partial 67 srf_emissions_inti src/chemistry/mozart/mo_srf_emissions.F90
file_touched_since_start=true
partial100-loc replenish chem2; fail-closed after job 6322529.desched1: no same-routine done proof in atm.log and/or native orchestration remains; overall_numeric_equal=True for lane but row not closed
partial 66 edgevpack src/dynamics/se/share/edge_mod.F90
file_touched_since_start=true
agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; edgevpack still owns native edge packing, reversal, buffer/derived-type mutation, and neighbor/corner logic; no same-routine Codon default body or BFB proof.
partial 58 longedgevpack src/dynamics/se/share/edge_mod.F90
file_touched_since_start=true
agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; longedgevpack still owns native long-edge packing, reversal and buffer/derived-type mutation; no same-routine Codon default body or fresh BFB proof.
partial 55 p_d_coupling src/dynamics/se/dp_coupling.F90
file_touched_since_start=true
agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; p_d_coupling remains large native physics-dynamics coupling orchestration with derived state, exchanges, and update loops; no same-routine Codon body/proof.
partial 49 stepon_run2 src/dynamics/se/stepon.F90
file_touched_since_start=true
agent w02 partial100-loc fail-closed 2026-05-31: no source change/commit; stepon_run2 remains large native timestep orchestration across dynamics/physics state, subcycles, timers, and exchanges; no same-routine Codon proof.
partial 37 set_srf_emissions src/chemistry/mozart/mo_srf_emissions.F90
file_touched_since_start=true
partial100-loc replenish chem2; fail-closed after job 6322529.desched1: no same-routine done proof in atm.log and/or native orchestration remains; overall_numeric_equal=True for lane but row not closed
partial 23 getcoags_wrapper_f src/chemistry/modal_aero/modal_aero_coag.F90
file_touched_since_start=true
agent w03 partial140 fail-closed; job 6315850.desched1 BFB pass overall_numeric_equal=True, but no same-routine atm.log proof for this routine; commit ce34ae0/a453bf7 only closes qqcw_set_ptr and qqcw_get_field
partial 23 preq_omega_ps src/dynamics/se/share/prim_si_mod.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 21 prim_advec_tracers_remap_rk2 src/dynamics/se/share/prim_advection_mod.F90
file_touched_since_start=true
partial100 closable6 recovery: restored partial after subagent 503/unvalidated lane state; no source commit, no fresh same-routine proof, no overall_numeric_equal=True closure for prim_advec_tracers_remap_rk2
partial 21 prim_step src/dynamics/se/share/prim_driver_mod.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 19 cam_run4 src/control/cam_comp.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 13 cam_run1 src/control/cam_comp.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 13 cam_run2 src/control/cam_comp.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 11 stepon_run1 src/dynamics/se/stepon.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 10 dyn_run src/dynamics/se/dyn_comp.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 9 cam_run3 src/control/cam_comp.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 6 remap1 src/dynamics/se/share/prim_advection_mod.F90
file_touched_since_start=true
agent w14_dynamics_se_lowloc partial200; left partial: remap1 active body is large native vertical remap with tridiagonal/monotonicity loops and abort/timer control; PPM branch delegates to remap_Q_ppm helper path, not a same-routine closure
partial 6 stepon_run3 src/dynamics/se/stepon.F90
file_touched_since_start=true
fail-closed 2026-05-31: restarted rw subagent hit 503 before validation; no source-only commit, no fresh same-routine atm.log proof, no overall_numeric_equal=True closure; restored partial.
partial 4 prim_advec_tracers_remap src/dynamics/se/share/prim_advection_mod.F90
file_touched_since_start=true
agent w08 partial200; left partial: fixed-case default dispatches to large native Prim_Advec_Tracers_remap_rk2 body; helper Codon coverage is not same-routine closure
partial 1 prim_advance_exp src/dynamics/se/share/prim_advance_mod.F90
file_touched_since_start=true
parallel partial35 integrated main d7474d3 fail-closed: no same-routine proof in integrated fixed case; native dycore orchestration remains

Generated by cam-codon-status · curated formula mapping + live routine statuses · 2026-06-01T19:24:15+00:00