diff --git a/docs/FEATURES.md b/docs/FEATURES.md index 20423e3..3982eec 100644 --- a/docs/FEATURES.md +++ b/docs/FEATURES.md @@ -35,6 +35,22 @@ Status legend: **planned**, **in progress**, **ported (validated)**, **deferred* | Constants and species table | `e3sm_src/modal_aero_data.F90`, `e3sm_src/shr_const_mod.F90` | compile-time + runtime indices hard-coded in `mam4_jax/data.py` (0-based, with sentinel `-1` for unused slots); provenance at `tests/reference/indices/reference.npz` | | Error function / special functions | `box_model_utils/error_function.F90`, `e3sm_src/shr_spfn_mod.F90` | use `jax.scipy.special` if available; otherwise port closed-form | +## CESM/CAM variant (plans 024/025, branch `feat/cam-driver`) + +The CAM code line shares leaf kernels with E3SM but none of the orchestration (`grep -rI amicphys` over CAM `src/` is empty). Reference: the sibling repo `mam-box-fortran` (CESM3 `cam6_4_187`), **fixdumfac** builds. All rows below are on `feat/cam-driver` (PR #74), not yet on `main`. + +| Feature | Fortran source | Status | +| --- | --- | --- | +| CAM topologies + parameters | read out of an initialised box model (not transcribable) | **landed** — `core/cam_topologies.py` (`cam_mam4`, `cam_mam5` incl. `coarse_strat`) + `core/cam_params.py` (per-type `specmw`, mechanism `adv_mass`, tracer names), both generated + sha-stamped; `tests/test_cam_{topology,params}.py` | +| Stratospheric sulfate equilibrium (`sulfeq` cluster) | `modal_aero_wateruptake.F90:895-1171` | **ported (validated)** — `physics/strat_sulfate.py`: Tabazadeh wt%, Ayers/Kulmala vapor pressure, dual Kelvin factors, + the reversible H2SO4 uptake consumer (`modal_aero_gasaerexch.F90:523-566`). Machine ε vs `tools/capture_sulfeq` (wtpct 1.3e-15, qeq 3.5e-14); upstream surf-tension interp bug preserved + written up | +| Mixed-phase table saturation (`estblf`/generic `qsat`) | `wv_saturation.F90` | **ported (validated)** — `physics/cam_saturation.py`; ~2× off the direct over-water formula at 200 K, which is why it exists separately | +| gasaerexch (SO4-only) | `modal_aero_gasaerexch.F90` | **ported (validated)** — `coupling/cam_driver.py`: third-variant uptake rates, fgain/reversible condensation, the legacy **8.0-monolayer** aging block, rename A1, tendency application. 1.1e-15 vs `tools/capture_gasaerexch`, both topologies | +| newnuc wrapper | `modal_aero_newnuc.F90:59-520` | **ported (validated)** — step-average H2SO4 reconstruction, table-qsat RH, cutoffs/floor/size constraints over the shared leafs. 2.0e-11 (ulp × J∝a¹⁰ amplification) vs `tools/capture_newnuc` | +| coag (`pair_option_acoag = 3`) | `modal_aero_coag.F90:73-990` | **ported (validated)** — three pairs, sequential three-branch number solves, aged-through aitken transfer with shell accounting, coag-side 8-monolayer aging, over the byte-identical `getcoags`. 6e-16 vs `tools/capture_coag`. Found + fixed en route: `shr_const_rgas` is the product 8314.467591, not 8314.46 | +| rename A1 (`no_acc_crs`) | `modal_aero_rename.F90:243-624` | **ported (validated)** — inside `cam_driver.py`; A2 (`acc_crs`) stays deferred (measured inert below `qso2` ~1e-5); references pinned `no_acc_crs` | +| calcsize / wateruptake topology threading | shared kernels | **landed** — optional `tables` bundles (E3SM default bit-identical); wateruptake gains `qv=` and the `strat=` wt%-composition water branch | +| CAM box driver | `mam_box_driver_cam.F90` | **ported (validated end-to-end)** — `cam_run_step`/`cam_run_timesteps`: SO2 stub → calcsize → sulfeq → wateruptake → mmr↔vmr → microphysics, substep loop wrapping the whole step (**default `n_substeps = 16`, ADR-021**; parity tests pin 1). 120 steps × {cam_mam4, cam_mam5} × {trop, strat}: every printed tracer at the reference's 7-digit print floor (~5e-7), total sulfur **4.5e-15**. `tests/test_cam_driver.py` | + ## Modes and species The MAM4-MOM (with `RAIN_EVAP_TO_COARSE_AERO`) reference configuration has four modes in this Fortran order (from `modal_aero_data.F90:104-109, 121-123`): diff --git a/docs/KEY_DECISIONS.md b/docs/KEY_DECISIONS.md index 077046d..716bdfd 100644 --- a/docs/KEY_DECISIONS.md +++ b/docs/KEY_DECISIONS.md @@ -335,3 +335,32 @@ Status values: **Accepted**, **Proposed**, **Superseded by ADR-NNN**. - **Keep the static per-call argument.** Rejected: it is the recompile-per-value and non-differentiable path, and it made the config surface two-headed (global + static kwarg) for one number. - **Put everything, selectors included, in one struct.** Rejected: `backend` and `mdo_*` must be static to select traced code; mixing them in would either force `static_argnums` on the whole struct — undoing the traced-leaf benefit — or require a `flax.struct.field(pytree_node=False)` dependency the package does not carry. - **Drop the `configure_*` globals entirely in favour of `params`.** Rejected for this PR: it is a breaking change for existing hosts and unrelated to pcarbon aging. Worth revisiting once `params` has usage. + +--- + +## ADR-021 — The CAM driver defaults to `n_substeps = 16`, deviating from reference-faithful defaults + +- **Status:** Accepted 2026-08-26 (owner: "I think 16 is the better number but we need to document it"). Plan 025 assumption A6, resolved. Introduced on `feat/cam-driver` (PR [#74](https://github.com/reflective-org/MAM4-JAX/pull/74)). +- **Context:** CAM couples MAM microphysics as an UN-SUBSTEPPED sequential chain (gasaerexch → newnuc → coag once per Δt; `aero_model.F90:1202-1247`), and that splitting does not converge while nucleation is active — nucleation and condensation compete for the same H₂SO₄ within the step, and the sequential split resolves the competition wrongly at coarse Δt. The Fortran box study measured a **2.08×** spread in accumulation sulfate across dt 120 s → 1.875 s (vs 1.3 % with nucleation off). The JAX driver (`coupling/cam_driver.py:cam_run_step`) wraps the WHOLE per-step physics in a substep loop, so `n_substeps = n` is semantically identical to running the box at `Δt/n`. +- **Measurement** (default scenario, dt = 30 s, error vs `n_substeps = 32`): + + | n_substeps | num_a2 | num_a1 | so4_a1 | h2so4 | cost | + |---|---|---|---|---|---| + | 1 (= CAM itself) | 26 % | 60 % | 57 % | 78 % | 1× | + | 2 | 16 % | 34 % | 31 % | 51 % | 2× | + | 4 | 9 % | 17 % | 16 % | 27 % | 4× | + | 8 | 4 % | 8 % | 7 % | 13 % | 8× | + | **16 (default)** | **1.4 %** | **2.5 %** | **2.2 %** | **4.4 %** | 16× | + + First-order convergence: the error halves per doubling; cost is linear. +- **Decision:** + 1. **`cam_run_step` / `cam_run_timesteps` default `n_substeps = 16`.** This is a deliberate deviation from the repo convention that defaults reproduce the reference (established in the PR #75 review): CAM's own behaviour (`n_substeps = 1`) is 26–78 % from the converged answer at a 30 s step, and shipping a known-O(50 %) configuration as the default answer was judged worse than deviating from the reference. 16 lands in the ~1.4–4.4 % band. + 2. **Reference parity is opt-in and pinned:** every parity test passes `n_substeps = 1` explicitly, and `tests/test_cam_driver.py` locks both the default value and the convergence direction/rate. + 3. The knob stays fully exposed; hosts trading accuracy for cost pick their own n with the table above. +- **Consequences:** + - A plain `cam_run_step(state)` is ~16× the reference's cost and does NOT bit-match the Fortran box; `n_substeps = 1` does (to the reference output's own 7-significant-digit print floor; total sulfur at 4.5e-15). + - The E3SM driver (`mam4_jax/driver.py`) is untouched — its amicphys path has its own substepping story (diffrax / ADR-013). +- **Alternatives considered:** + - **Default 1 (reference-faithful).** Rejected by the owner: this driver exists to produce usable answers, and the un-substepped splitting error dwarfs every other error source in the port by ~5 orders of magnitude. + - **Default 8.** Rejected: still 4–13 % from converged; 16's ~2 % is the first rung that is small against typical host-model uncertainty, at a cost that is still trivial for a box model. + - **Adaptive substepping.** Out of scope here (that is the diffrax branch's approach on the E3SM side); a fixed count keeps the CAM driver structurally faithful to "CAM at a finer dt". diff --git a/docs/PROGRESS.md b/docs/PROGRESS.md index 3af9766..05689dc 100644 --- a/docs/PROGRESS.md +++ b/docs/PROGRESS.md @@ -5,6 +5,16 @@ A running, append-only log of project milestones. Most-recent entry on top. Upda Each entry: date, short title, links to commits / PRs, one-paragraph summary. --- +## 2026-08-25/26 — CAM driver: sulfeq cluster + full CAM chain, end-to-end validated; MAM5's first physics (branch `feat/cam-driver`) + +- PR: [#74](https://github.com/reflective-org/MAM4-JAX/pull/74) (open — owner is holding merges to `main`). Plan: `docs/plans/025-cam-driver.md` §6–7 (G0–G5, all done). Merged `main`@v0.4.0 and PR #73's topology branch into the branch en route. +- **What landed**: the complete CESM/CAM driver for the SO4-only box scope — see the new "CESM/CAM variant" section in `FEATURES.md` for the per-component table. Every component validated against fresh captures of the real Fortran (five new `tools/capture_*` in `mam-box-fortran`), both topologies, machine ε at each layer; end-to-end 120-step trajectories match the fixdumfac reference builds at the reference's own print floor with total sulfur at 4.5e-15. This is the first time `cam_mam5` (incl. `coarse_strat`) produced physics against an independent reference. +- **ADR-021**: `n_substeps` defaults to 16 (owner decision) — CAM's own un-substepped splitting is 26–78% from converged at dt=30 s with nucleation active; a deliberate, documented deviation from the defaults-reproduce-the-reference convention. Parity tests pin `n_substeps=1`. +- **Findings recorded**: the box reference's `is_first_step()` shim is true every step, so the lagged-wet-diameter sulfeq feedback does not exist in the reference (`reseed_dgnwet_each_step` exposes both behaviours); `shr_const_rgas` is the product 8314.467591 (the rounded 8314.46 cost 2e-6 in the coag number solves); upstream surf-tension interpolation bug in `calc_h2so4_equilib_mixrat` (written up in `mam-box-fortran/docs/bugs/`); CAM's `gas_aer_uptkrates` is a third variant, distinct from both E3SM ports. +- Suite: **270 passed**. + +--- + ## 2026-08-25 — Primary-carbon aging + float32-safe coagulation mass transfer (`main`) diff --git a/docs/figures/cam_vs_e3sm.png b/docs/figures/cam_vs_e3sm.png new file mode 100644 index 0000000..6fbc358 Binary files /dev/null and b/docs/figures/cam_vs_e3sm.png differ diff --git a/docs/plans/025-cam-driver.md b/docs/plans/025-cam-driver.md new file mode 100644 index 0000000..3331a92 --- /dev/null +++ b/docs/plans/025-cam-driver.md @@ -0,0 +1,356 @@ +# Plan 025 — CAM driver (plan 024 PR G), and what it can legitimately reuse + +**Status:** IN PROGRESS. Written 2026-08-21 while the owner was away; every +assumption is listed in §5 for review rather than buried in code. + +**Scope, per owner 2026-08-20:** box model only. Coagulation, condensation, +nucleation. **No deposition, no column transport, no evaporation** — evaporation +is an organics process, not a sulfate one (see `mam-box-fortran` +`docs/design/SO4_SCOPE.md`). SO4-only species set. + +--- + +## 1. The question that had to be answered first + +`coupling/amicphys.py` already contains standalone helpers for all four +processes — `_mam_gasaerexch_1subarea`, `_mam_rename_1subarea`, +`_mam_newnuc_1subarea`, `_mam_coag_1subarea`. The tempting move is to wire them +into CAM's sequence and call it a CAM driver. + +**That would be CAM's *sequencing* with E3SM's *kernels*.** Whether it is +legitimate has to be settled per process, not assumed. Using the per-process +discrepancy reports in `mam-box-fortran/docs/reference/discrepancies/`, plus one +new numerical check: + +| Process | Reusable for CAM? | Basis | +| --- | --- | --- | +| **Uptake rates** (`gas_aer_uptkrates`) | ❌ **No — corrected in §7** | CAM vs E3SM-legacy is bit-identical (58/58), but the JAX port implements the *amicphys* variant, a third one (Knudsen-dependent β vs CAM's fixed β=2, exact vs truncated constants, ac handling). CAM's must be ported | +| **Condensation, H2SO4, tropospheric** | ✅ **Yes — verified numerically** | See §2 | +| **Condensation, H2SO4, `sulfate_equilib`** | ❌ **No** | CAM-only. No E3SM counterpart exists to have been ported | +| **Coagulation** | ✅ **Yes** | `getcoags` is **byte-for-byte identical** between CAM and E3SM — comments and whitespace included — over 1519 lines | +| **Nucleation** | ✅ **Yes, in a box** | Leaf parameterisations are 0-diff with exact literal matches. The one answer-changing difference (V2) is **cloud handling**, and a box model runs `cld = 0`, where both reduce to the same thing. See assumption A4 | +| **Rename** | ❌ **No** | CAM's default path (**A1**) and E3SM's production path (**C**) are "a real algorithmic difference". The JAX port ports **C**. See §3 | + +**So exactly two things need new science work: `sulfate_equilib` condensation, +and rename.** Everything else is already in this repo and correct for CAM. + +## 2. Tropospheric H2SO4 condensation is the same maths + +CAM (`modal_aero_gasaerexch.F90`): + +```fortran +sum_uprt_so4 = Σ_n uptkratebb(n) ! :407-408 +avg_uprt_so4 = (1 - exp(-dt*sum_uprt_so4))/dt ! :492 +sum_dqdt_so4 = q(l_so4g) * avg_uprt_so4 ! :503 +dqdt_so4(n) = fgain_so4(n) * sum_dqdt_so4 ! :567-569 + where fgain_so4(n) = uptkratebb(n)/sum_uprt_so4 +``` + +JAX `_linear_uptake_closed_form` solves `dg/dt = -Kg + src`, +`da_i/dt = uptk_i·g` with `K = Σ uptk_i` — the same competing-sink system. With +`src = 0` the two are algebraically identical, since +`uptk_i·g_avg·dt = (uptk_i/K)·g0·(1-e^{-K dt})`. + +**Checked numerically rather than left as algebra:** 200 random cases over +`uptk ∈ [1e-6, 1e-2]`, `g0 ∈ [1e-14, 1e-9]`, `dt ∈ [1, 1000]` s — worst relative +difference **1.01e-14**. Identical to round-off. + +`src = 0` is the right setting for CAM: CAM does not add gas production inside +gasaerexch. It arrives as `del_h2so4_gasprod`, which the driver hands to +*nucleation*, not to condensation. See assumption A2. + +## 3. Rename is the real blocker + +From the rename report's legend: + +| Tag | Code | +| --- | --- | +| **A1** | `modal_aero_rename_no_acc_crs_sub` — **CAM's default** | +| **A2** | `modal_aero_rename_acc_crs_sub` — CAM, `modal_accum_coarse_exch=.true.` | +| **B** | E3SM **legacy** `modal_aero_rename_sub` (dead code in E3SM) | +| **C** | E3SM **production** `mam_rename_1subarea`, inside amicphys | +| **J** | the JAX port — **ports C** | + +Verdict: *"A1 vs B is a non-difference. A1 vs C is a real algorithmic +difference."* A1 and B are line-for-line identical — 27 differing lines out of +243, **zero of which change the arithmetic**. + +So the existing JAX rename cannot serve CAM. But because **A1 ≡ B**, porting +CAM's rename is a single well-defined job that also gives E3SM's legacy path for +free. + +This matters more than it looks: rename is what produced the ×31 accumulation- +number jump in the Fortran box runs. A driver without it, or with the wrong one, +is not approximately right — it is qualitatively different. + +## 4. What this PR does and does not do + +**Does:** the CAM sequence — `gasaerexch` (tropospheric H2SO4) → `newnuc` → +`coag` — on grid-cell means, with sub-stepping exposed, reusing only the kernels +established above as legitimate. + +**Does not:** rename, or the `sulfate_equilib` branch. Both raise rather than +silently substituting an E3SM equivalent, because a wrong-but-running driver is +worse than one that refuses. + +**Sub-stepping is exposed and defaults ON**, against CAM's own behaviour. The +Fortran showed a **2.08× spread** in accumulation sulfate across dt 120 s → 1.875 s +with nucleation active, versus 1.3 % with it off. Faithfully reproducing CAM's +un-substepped splitting means reproducing an O(50 %) error at a 30 s step. See +assumption A6 — this is a deliberate divergence and needs owner sign-off. + +## 5. Assumptions — all of them, for review + +Numbered so they can be accepted or rejected individually. + +| # | Assumption | Why | Risk if wrong | +| --- | --- | --- | --- | +| **A1** | Reusing E3SM-derived kernels for CAM is legitimate **only** where the discrepancy reports say the code is identical, and I have not re-verified those reports beyond the two checks in §2 | The reports carry `file:line` citations and were written from the sources | Moderate. A report being wrong would put wrong physics in a "CAM" driver | +| **A2** | `src = 0` inside CAM's gasaerexch; gas production reaches *nucleation* via `del_h2so4_gasprod`, not condensation | Matches `aero_model.F90`'s call sequence and the Fortran box driver already built | Low — verified in the coupling module | +| **A3** | SO4-only means the SOA differences (`opoa_frac`, volatility) are out of scope, so "the 58-line kernel is all that's shared" is pessimistic for our case | Owner scope 2026-08-04 and 2026-08-20 | Low | +| **A4** | Nucleation's cloud-handling difference vanishes because the box runs `cld = 0` | Both formulations weight by `(1-cld)` or area-weight by `fclea`; at `cld = 0` both give the full clear-sky result | **Should be tested**, not assumed. Listed as work below | +| **A5** | Rename must be CAM's A1, not E3SM's C, and A1 ≡ B makes it one port | Rename report verdict | Low on the verdict; the port itself is unwritten and untested | +| **A6** | Sub-stepping should default **ON**, diverging from CAM | dt-convergence measurement | **This is a science-policy call, not a technical one.** Needs owner sign-off | +| **A7** | `cam_mam4`/`cam_mam5` from PR #73 are the right topologies | Read out of an initialised CAM model; losslessness verified | Low | +| **A8** | Grid-cell means, no sub-areas, is right for CAM | CAM has no sub-area concept — `grep -rI amicphys` over CAM `src/` returns zero hits | Low | + +## 6. Progress and remaining work + +### Done + +1. ✅ **A4 tested, and it turned up a defect instead.** The JAX port implements + only the clear-sky sub-area, so at `cld = 0` it trivially matches CAM's + `(1-0) × clear` — A4 holds. But `_mam_amicphys_1gridcell`'s docstring + *claimed* a non-zero cloud fraction "raises a clear error"; the code declined + to check and never read `cldn` at all, so a cloudy cell silently got + clear-sky physics applied to the whole cell. Fixed, and the guard had to move + **outside** the jit: `driver.run_step` is `@jax.jit`, so a check inside it + could never fire. + +2. ✅ **CAM rename implemented as a selector**, not a second implementation — + E3SM's code contains CAM's algorithm as its `optaa /= 40` branch, and every + quantity it needs was already computed. Default stays `"e3sm"`, asserted. + +3. ✅ **Reference capture built** (`mam-box-fortran/tools/capture_rename`), five + growth values. Two mistakes worth recording: rename is **growth-driven**, so + the first capture with `dqdt = 0` produced an all-zero transfer that looked + like a valid reference; and zsh's lack of word-splitting silently pinned the + growth parameter, which made the mass transfer look constant across a sweep. + +### Validated, and precisely how far + +Compared on **dimensionless** transfer fractions rather than by mapping CAM's +`q`/`dqdt` into the amicphys-local view. That mapping is where a factor-of-1000 +error produces a *fake* validation — either failing for the wrong reason, or +passing because two errors cancel. Both inputs (`v2n/voltonumb`, `deldryvol/dryvol`) +and outputs (`xferfrac_num`, `xferfrac_vol`) are unit-free, so no conversion +appears anywhere. + +**Worst relative difference across five growth values: 9.6e-10** — the floor the +reference's 9 significant figures can resolve. + +Those five points sit in a regime where **both branches agree exactly**, so +they validate the machinery the two algorithms *share* — erfc tail integrals, +`dp_cut`, `factoraa`/`factoryy`, the transfer-fraction clamps. Necessary, not +sufficient. + +### ✅ And now validated where they DIVERGE — machine precision + +The divergent window had to be **derived**, not searched for: + +``` +E3SM clamps when dgn_t_old > dp_belowcut (= 0.99 · dp_cut) +CAM clamps when dgn_t_new >= dp_cut + with dgn_t_new = dgn_t_old · (1+growth)^(1/3) +``` + +so divergence needs an **oversized mode with small growth** — `dgn_t_old` just +above `dp_belowcut` while `dgn_t_new` stays below `dp_cut`, which bounds growth +under about 3 %. Confirmed behaviourally: at `dgn_old = 8.12e-8` the branches +diverge at growth 0.005 and 0.01 and then **converge again at 0.03**, exactly +where the derivation says they should. + +Result over six points (two diameters × three growth values): + +| | vs CAM's Fortran | +| --- | --- | +| **JAX `method="cam"`** | **worst 8.1e-15** — machine precision | +| JAX `method="e3sm"` | off by **68 % to 308 %** | + +So the comparison genuinely discriminates: a `method="cam"` that silently fell +through to the E3SM path would fail by orders of magnitude, and there is a test +asserting that. + +⚠ Getting there needed a **units fix in the capture tool**. Rename's +`dryvol_t_old` is in m³-AP/kmol-air — `q·(specmw/specdens)`, not raw `q`. +Parameterising by raw volume put the intended `v2n` an order of magnitude below +the `v2nhirlx` floor, so `num_t_oldbnd` clamped every input to the same value: +two visibly different states (v2n 4.090e20 and 9.695e20) produced +**byte-identical output with no error anywhere.** + +### ✅ The sulfeq equilibrium cluster — ported and validated at machine precision + +The `sulfate_equilib` work splits in two: the EQUILIBRIUM VALUE (computed per +mode inside CAM's water uptake) and its CONSUMPTION (the reversible +condensation branch in gasaerexch). The first half is done: + +- `mam4_jax/physics/strat_sulfate.py` ports `calc_h2so4_wtpct` (Tabazadeh + 1997 composition) + `calc_h2so4_equilib_mixrat` (Ayers/Kulmala vapor + pressure, Giauque enthalpy, dual Kelvin factors) + the CAM `qsat_water` + they stand on — which is NOT the already-ported E3SM box `qsat_water`: + CAM returns `qs = 1` whenever `p <= es`, the E3SM box clamps only a + negative-denominator `qs`, and they disagree on `es ∈ [p, p/(1−ε)]` + (reachable at the routine's own `t = 450 K` clamp). +- The routines were **private** to `modal_aero_wateruptake`; exposed by a + visibility-only patch applied to a staged copy by the new + `mam-box-fortran/tools/capture_sulfeq` (the box model's process masks + cannot isolate them — they only run under `modal_strat_sulfate`, deep in + the wateruptake driver). +- The capture grid pins every branch by construction: both T clamps + (135→140, 460→450 K), all three Tabazadeh activity regimes plus both + activity clamps (qh2o is BUILT as `activ_target × qs`, so regime coverage + cannot drift with T/p), and Kelvin-strong→negligible diameters (1e-8 → + 9e-7 m, the MAM5 `coarse_strat` dgnum). 27 qsat + 189 wtpct + 567 full + cases → `tests/reference/cam_sulfeq/sulfeq.json`. +- **Measured worst relative errors** (`tests/test_strat_sulfate.py`): + wtpct **1.3e-15**, sulden **7.1e-16**, qh2so4_equilib **3.5e-14** (the + ~100-magnitude exponent inside `exp` amplifies its last ULP by ~1e-14 — + gated at 5e-13). Plus Kelvin monotonicity in diameter and reverse-mode + gradient finiteness across every branch. +- ⚠ **Upstream defect found while porting, preserved faithfully**: the + first surface-tension interpolation pairs knot `i−1`'s ordinate with knot + `i`'s abscissa (`surf_tens = sig1 + dsigma_dwt*(wtpct_flat - stwtp(i))`, + F90:1005), offsetting the whole segment by `−(sig2−sig1)`. Both sibling + lookups in the same routine are correct. Written up in mam-box-fortran + `docs/bugs/BUG-cam-wateruptake-surftens-interp.md`; the port keeps + bit-parity with the bug. + +### ✅ The reversible condensation branch (the cluster's consumer) + +`h2so4_reversible_uptake` (same module) ports +modal_aero_gasaerexch.F90:523-566: exponential decay of the gas toward the +mode-weighted equilibrium `g_equ = Σ(uptk·sulfeq)/Σuptk`, per-mode +`dqdt = uptk·(g_avg − sulfeq)` with the `a_end ≥ 0` evaporation floor, the +`kxt < 1e-5` first-order branch, the `deltatxx = deltat·(1+1e-15)` nudge, +and the three-state `ido_so4a` mode classification (1 = has slot, 2 = CAM's +slotless pcarbon age-source, 0 = inactive). Validated against a verbatim +NumPy transcription of the Fortran (loops, `1-exp`, cycles) over 300 +randomized states spanning both branches, condensation/evaporation, the +floor, and all ido classes — bar 5e-11, sized by the one documented +arithmetic deviation (`-expm1(-kxt)`, repo-standard per plan 026/ADR-019, +worth ~2e-11 at the branch threshold). Exact-zero equilibrium fixed point, +floor semantics, branch continuity, and reverse-mode grads locked in. +When the driver lands, the end-to-end comparison (item 2 below) validates +this against the actual Fortran box rather than a transcription. It needs +the mode-mean `dmean = dgncur_awet·exp(1.5·alnsg²)` from the PREVIOUS step +— the lagged carried state plan 024 §6 describes. + +### Remaining, in order + +1. **The driver itself** — CAM's sequence on grid-cell means, sub-stepping + exposed. +2. **Reference comparison** against `mam-box-fortran` at a pinned tag, for both + `cam_mam4` and `cam_mam5`. + +### Assumptions added since §5 was written + +| # | Assumption | Status | +| --- | --- | --- | +| **A9** | Comparing dimensionless fractions is sufficient to validate the algorithm | ✅ **Confirmed.** Avoids the unit mapping entirely, and the divergent-regime points show it discriminates | +| **A10** | The five original capture points are representative | ❌ **Was wrong, now fixed.** They all sat in the saturated regime where both branches agree. Six divergent-regime points added | +| **A11** | `qaer_cur` is post-growth and the delta is informational | Verified against the Fortran reference: it conserves against `qaer_cur` to 0.0 and against `qaer_cur + delta` to 2.4e-3 | + +--- + +## 7. The driver itself — sub-plan (started 2026-08-26, owner go-ahead "Let's do it") + +**A6 is resolved**: owner approved proceeding with the driver including +sub-stepping exposed and defaulting ON (2026-08-26). The default substep +COUNT is still to be picked empirically in G5 (smallest n bringing a 30 s +step within ~1 % of the converged answer on the reference scenario). + +### Findings from the source read that reshape §1's table + +- **A1 correction — CAM's `gas_aer_uptkrates` is a THIRD variant, not the + ported one.** The "bit-identical 58/58" claim compared CAM against + E3SM-*legacy*. The JAX port (`_gas_aer_uptkrates_1box1gas`) implements + the *amicphys* variant: Knudsen-dependent β, caller-supplied + accommodation/diffusivity/free path, exact √π/√2. CAM's + (modal_aero_gasaerexch.F90:953-1086): **fixed β = 2**, hardcoded + ac = 0.65 literals (`0.4875`, `1.184`), truncated `tworootpi = 3.5449077` + / `root2 = 1.4142135`, its own `gasdiffus = 0.557e-4·T^1.75/p`, + `gasspeed = 14.70·√T`, and the result is multiplied by number + concentration and gasdiffus inside. Must be ported, not reused. +- **The legacy 8.0-monolayer aging runs INSIDE CAM's gasaerexch** (:719-806, + `modefrm_pcage` block, `dr_so4_monolayers_pcage` from the gasaerexch + module parameter = **8.0**), and AGAIN inside `modal_aero_coag_sub` for + the coagulated shell (modal_aero_coag.F90:502-546). This closes the + #75-review attribution question for good: the CAM code line genuinely + ages at 8.0 through the legacy path; E3SM/amicphys receives 3.0 via + phys_control. Both are now facts of their respective drivers, not a knob + disagreement. +- **`DGNUM` pbuf-initialises to 0.0** (modal_aero_calcsize.F90:131), so a + reference run with calcsize/wateruptake off is garbage — END-TO-END + parity requires topology-threaded calcsize + wateruptake (the deferred + plan-024 PR C "~66 call sites" job, scoped to what the driver calls). + The MICROPHYSICS sequence (gasaerexch → newnuc → coag) can be validated + first against isolated captures, which need no calcsize. +- ~~The box's `troplev = pver` asymmetry means Köhler-only water uptake~~ + **CORRECTED during G5**: under `strat` the box driver calls + `tropopause_set_box_level(pver+1)` (mam_box_driver_cam.F90:182), so + wateruptake's `k < troplev` strat branch IS live — the wt%-composition + solution volume replaces Köhler for every mode. Ported as + `wateruptake(strat=...)`. +- **MAM5 reference runs pin `nl_acc_crs = 0`** — the box defaults + `modal_accum_coarse_exch` to ON under MAM5, but rename-A2 (636 lines) + stays deferred per plan 024 (measured inert below qso2 ~1e-5); the + reference must be captured with the same setting the port implements. +- **PR #73's branch (`feat/cam-mam5-topology`) is merged into this branch** + — the driver is the first real consumer of `CAM_MAM4`/`CAM_MAM5`. The + topologies carry no molecular weights; `specmw_amode`/`adv_mass` must be + dumped from the initialised box model like the index tables were (same + argument: `adv_mass` comes from the chemistry preprocessor). + +### Commit-sized steps + +| Step | Content | Validation | +| --- | --- | --- | +| **G0** ✅ | Extend `mam-box-fortran/tools/dump_tables` to emit per-slot `SPECMW_AMODE`, the gas-window `ADV_MASS`, `CNST_NAMES`, `MWDRY`; regenerate both topologies; land the values as `mam4_jax/core/cam_params.py` (generated, sha-stamped) | **Done.** `tests/test_cam_params.py`: alignment, every pointer resolving to the right tracer NAME, plan 024 §3 census values, mechanism gas MWs | +| **G1** ✅ | `mam4_jax/coupling/cam_driver.py`: CAM `gas_aer_uptkrates` (third variant) + SO4-only `gasaerexch_cam` — fgain/avg_uprt trop path, reversible strat path (ported), the gasaerexch aging block at 8.0, rename-A1 call, tendency application. All topology-threaded (`Topology` argument; tables cached per name) | **Done.** `tools/capture_gasaerexch` (24 branch-pinning cases × both topologies, real `modal_aero_gasaerexch_sub`, prescribed diameters): worst rel-err **1.1e-15** on every quantity that is not a cancellation sliver of its own input. The post-aging pcarbon number (a `q·10ε` remnant) differs up to ~5% *of the sliver* (~1e-15 of the tracer): the reference binary FMA-contracts `q + dqdt·Δt` (gfortran `-O2`, arm64 `-ffp-contract=fast`) — verified bit-for-bit by reproducing both chains — so the bar is rtol 5e-13 + per-slot atol `1e-13·q_in`. Parity over the FULL Fortran subroutine also confirms **A13** (zero SOA is a soaexch fixed point) empirically | +| **G2** ✅ | CAM `modal_aero_newnuc_sub` wrapper over the ported nucleation leafs (`del_h2so4_gasprod`/`aeruptk` semantics; `mw_so4a_host` threaded into the dispatcher as an optional arg exactly as the Fortran passes it — E3SM default untouched). Includes `physics/cam_saturation.py`: CAM's generic `qsat` is the mixed-phase TABLE (`estblf`, 250 entries, water/ice blend over 20 K) — NOT the direct over-water formula (~2× apart at 200 K) | **Done.** `tools/capture_newnuc` (96 cases × both topologies): worst rel-err **2.0e-11**, the ~1-ulp form differences (`expm1`, table interp) amplified by nucleation's ~10th-power H2SO4/RH sensitivity; gated 1e-10. Sulfur closure exact per case; cutoff/floor gates exercised both ways | +| **G3** ✅ | CAM `modal_aero_coag_sub` port (pair_option 3: ait→acc, pca→acc, ait→pca-effective-accum + coag-side 8-monolayer aging), reusing `getcoags_wrapper_f` | **Done.** `tools/capture_coag` (32 cases × both topologies, all three number-solve branches, saturated + fractional aging): worst non-sliver rel-err **6e-16**. Found en route: `shr_const_rgas` is the PRODUCT `6.02214e26·1.38065e-23 = 8314.467591` — the rounded `8314.46` was 9.1e-7 off and the implicit number solves amplified it to ~2e-6. Conservation/monotonicity/untouched-mode (coarse, coarse_strat) invariants asserted | +| **G4a** ✅ | `mam_microphysics_cam`: the exact one-call chain gasaerexch → newnuc → coag with the `del_h2so4_aeruptk` positive-down bookkeeping (aero_model.F90:1191-1214). Sub-stepping deliberately NOT here — it wraps the whole per-step physics in the driver so `n_substeps = n` ≡ running the box at `deltat/n`, the exact quantity the Fortran dt-study varied | **Done.** `tools/capture_microphys` (12 cases × both topologies, trop + both strat kinds): worst non-sliver rel-err **1.5e-12** (the G1-G3 ulp differences compounded through three chained stages). Sulfur closure through the chain at 1e-13; a test proves the aeruptk bookkeeping is live (zeroing it changes the answer) | +| **G4b** ✅ | calcsize + wateruptake threaded via optional `tables` bundles (`CalcsizeTables`/`WateruptakeTables`; `None` default = the E3SM module constants, bit-identical — suite proves it); wateruptake gains `qv=` (CAM keeps water vapor outside the aerosol window) and `strat=` (the wt%-composition solution-volume branch, wateruptake_sub:583-591 — live in the box because the driver sets its tropopause above the single level); `cam_run_step`/`cam_run_timesteps` assemble SO2 stub → calcsize → sulfeq → wateruptake → mmr↔vmr → microphysics, substep loop wrapping the WHOLE step | **Done.** See G5 | +| **G5** ✅ | End-to-end vs the `mam-box-fortran` **fixdumfac** builds: {cam_mam4, cam_mam5} × {trop, strat}, all-default namelist, 120 steps × dt 30 s | **Done — first MAM5 physics against an independent reference.** Every printed tracer within the reference's own 7-significant-digit print floor (~5e-7; gated 2e-6); the one full-precision column, total sulfur, agrees at **4.5e-15** on all four trajectories. `tests/test_cam_driver.py` + `tests/reference/cam_box/` | +| **G5** | End-to-end vs `mam-box-fortran` at a pinned tag: `cam_mam4` and `cam_mam5` (`nl_acc_crs=0`), trop + strat scenarios; pick the substep default empirically | acceptance bar proposed after measuring, ADR to record it | + + +### G5 findings (2026-08-26) + +1. **The lagged-`dgncur_awet` feedback never survives a step in the box + reference**: the vendored time-manager shim's `is_first_step()` is TRUE + every step (`time_manager.F90:13-22`; the driver never advances it), so + wateruptake re-seeds `dgncur_awet = dgncur_a` each step and sulfeq is + computed from fresh post-calcsize DRY diameters. Production CAM lags + genuinely. The port exposes `reseed_dgnwet_each_step` (default True = + the reference's behaviour); before this was found, the strat trajectory + was 2x off by step 9. +2. **A6 substep measurement** (dt=30 s, default scenario, vs n=32): + + | n_substeps | num_a2 | num_a1 | so4_a1 | h2so4 | + |---|---|---|---|---| + | 1 (CAM-faithful) | 26% | 60% | 57% | 78% | + | 2 | 16% | 34% | 31% | 51% | + | 4 | 9% | 17% | 16% | 27% | + | 8 | 4% | 8% | 7% | 13% | + | 16 | 1.4% | 2.5% | 2.2% | 4.4% | + + First-order splitting, exactly the Fortran study's 2.08x finding. + **RESOLVED 2026-08-26 — owner picked `n_substeps = 16` as the default** + ("I think 16 is the better number but we need to document it"), + accepting the deliberate deviation from the defaults-reproduce-the- + reference convention. Documented as **ADR-021** (with this table); + every parity test opts back into `n_substeps = 1` explicitly, and + `test_documented_defaults` locks the value. A6 is closed. +3. The E3SM path is bit-unchanged by the threading (the `tables=None` + defaults are the same module constants; full suite green throughout). diff --git a/mam4_jax/core/cam_params.py b/mam4_jax/core/cam_params.py new file mode 100644 index 0000000..50d3ba4 --- /dev/null +++ b/mam4_jax/core/cam_params.py @@ -0,0 +1,168 @@ +"""CAM per-configuration parameters — GENERATED, do not hand-edit. + +Produced by `tools/dump_tables/to_params.py` in the sibling repo +`mam-box-fortran`; same provenance chain as `cam_topologies.py` +(read out of an initialised CAM MAM box model — `specmw_amode` and +`adv_mass` come from the chemistry preprocessor and are not +transcribable from source). Regenerate alongside the topologies: + tools/dump_tables/run.sh mam4 > outputs/tables/cam_mam4_indices.py + tools/dump_tables/run.sh mam5 > outputs/tables/cam_mam5_indices.py + python3 tools/dump_tables/to_params.py +""" +from __future__ import annotations + +CAM_PARAMS: dict = { + # source: cam_mam4_indices.py sha256: 1dd51e380a38ea35… + "cam_mam4": { + "loffset": 5, + "gas_pcnst": 26, + "mwdry": 28.966, + # per species TYPE, aligned with Topology.specname_amode ('so4', 'pom', 'soa', 'bc', 'dst', 'ncl') + "specmw_amode": (115.10734, 12.011, 12.011, 12.011, 135.064039, 58.442468), + # chemistry-mechanism molecular weights, gas window (tracer slots loffset..pcnst-1) + "adv_mass": ( + 12.011, # bc_a1 + 12.011, # bc_a4 + 62.1324, # DMS + 135.064039, # dst_a1 + 135.064039, # dst_a2 + 135.064039, # dst_a3 + 34.0136, # H2O2 + 98.0784, # H2SO4 + 58.442468, # ncl_a1 + 58.442468, # ncl_a2 + 58.442468, # ncl_a3 + 1.0074, # num_a1 + 1.0074, # num_a2 + 1.0074, # num_a3 + 1.0074, # num_a4 + 12.011, # pom_a1 + 12.011, # pom_a4 + 64.0648, # SO2 + 115.10734, # so4_a1 + 115.10734, # so4_a2 + 115.10734, # so4_a3 + 12.011, # soa_a1 + 12.011, # soa_a2 + 12.011, # SOAE + 12.011, # SOAG + 18.0142, # H2O + ), + "cnst_names": ('bc_a1', 'bc_a4', 'DMS', 'dst_a1', 'dst_a2', 'dst_a3', 'H2O2', 'H2SO4', 'ncl_a1', 'ncl_a2', 'ncl_a3', 'num_a1', 'num_a2', 'num_a3', 'num_a4', 'pom_a1', 'pom_a4', 'SO2', 'so4_a1', 'so4_a2', 'so4_a3', 'soa_a1', 'soa_a2', 'SOAE', 'SOAG', 'H2O'), + }, + # source: cam_mam5_indices.py sha256: 9a4b4a28e7206bc7… + "cam_mam5": { + "loffset": 5, + "gas_pcnst": 103, + "mwdry": 28.966, + # per species TYPE, aligned with Topology.specname_amode ('so4', 'pom', 'soa', 'bc', 'dst', 'ncl') + "specmw_amode": (115.10734, 12.011, 12.011, 12.011, 135.064039, 58.442468), + # chemistry-mechanism molecular weights, gas window (tracer slots loffset..pcnst-1) + "adv_mass": ( + 12.011, # bc_a1 + 12.011, # bc_a4 + 79.904, # BR + 115.3567, # BRCL + 95.9034, # BRO + 141.90894, # BRONO2 + 99.71685, # BRY + 153.8218, # CCL4 + 165.364506, # CF2CLBR + 148.91021, # CF3BR + 137.367503, # CFC11 + 187.37531, # CFC113 + 170.921013, # CFC114 + 154.466716, # CFC115 + 120.913206, # CFC12 + 173.8338, # CH2BR2 + 30.0252, # CH2O + 94.9372, # CH3BR + 133.4023, # CH3CCL3 + 50.4859, # CH3CL + 47.032, # CH3O2 + 48.0394, # CH3OOH + 16.0406, # CH4 + 252.7304, # CHBR3 + 35.4527, # CL + 70.9054, # CL2 + 102.9042, # CL2O2 + 51.4521, # CLO + 97.45764, # CLONO2 + 100.91685, # CLY + 28.0104, # CO + 44.0098, # CO2 + 66.007206, # COF2 + 82.461503, # COFCL + 62.1324, # DMS + 135.064039, # dst_a1 + 135.064039, # dst_a2 + 135.064039, # dst_a3 + 18.998403, # F + 1.0074, # H + 2.0148, # H2 + 259.823613, # H2402 + 34.0136, # H2O2 + 98.0784, # H2SO4 + 80.9114, # HBR + 116.948003, # HCFC141B + 100.493706, # HCFC142B + 86.467906, # HCFC22 + 36.4601, # HCL + 20.005803, # HF + 63.01234, # HNO3 + 79.01174, # HO2NO2 + 96.9108, # HOBR + 52.4595, # HOCL + 14.00674, # N + 44.01288, # N2O + 108.01048, # N2O5 + 58.442468, # ncl_a1 + 58.442468, # ncl_a2 + 58.442468, # ncl_a3 + 30.00614, # NO + 46.00554, # NO2 + 62.00494, # NO3 + 1.0074, # num_a1 + 1.0074, # num_a2 + 1.0074, # num_a3 + 1.0074, # num_a4 + 1.0074, # num_a5 + 15.9994, # O + 31.9988, # O2 + 47.9982, # O3 + 47.9982, # O3S + 67.4515, # OCLO + 60.0764, # OCS + 12.011, # pom_a1 + 12.011, # pom_a4 + 32.066, # S + 146.056419, # SF6 + 48.0654, # SO + 64.0648, # SO2 + 80.0642, # SO3 + 115.10734, # so4_a1 + 115.10734, # so4_a2 + 115.10734, # so4_a3 + 115.10734, # so4_a5 + 12.011, # soa_a1 + 12.011, # soa_a2 + 12.011, # SOAG + 0.000548567, # e + 33.0062, # HO2 + 14.00674, # N2D + 28.01348, # N2p + 30.00614, # NOp + 14.00674, # Np + 15.9994, # O1D + 31.9988, # O2_1D + 31.9988, # O2_1S + 31.9988, # O2p + 17.0068, # OH + 15.9994, # Op + 15.9994, # Op2D + 15.9994, # Op2P + 18.0142, # H2O + ), + "cnst_names": ('bc_a1', 'bc_a4', 'BR', 'BRCL', 'BRO', 'BRONO2', 'BRY', 'CCL4', 'CF2CLBR', 'CF3BR', 'CFC11', 'CFC113', 'CFC114', 'CFC115', 'CFC12', 'CH2BR2', 'CH2O', 'CH3BR', 'CH3CCL3', 'CH3CL', 'CH3O2', 'CH3OOH', 'CH4', 'CHBR3', 'CL', 'CL2', 'CL2O2', 'CLO', 'CLONO2', 'CLY', 'CO', 'CO2', 'COF2', 'COFCL', 'DMS', 'dst_a1', 'dst_a2', 'dst_a3', 'F', 'H', 'H2', 'H2402', 'H2O2', 'H2SO4', 'HBR', 'HCFC141B', 'HCFC142B', 'HCFC22', 'HCL', 'HF', 'HNO3', 'HO2NO2', 'HOBR', 'HOCL', 'N', 'N2O', 'N2O5', 'ncl_a1', 'ncl_a2', 'ncl_a3', 'NO', 'NO2', 'NO3', 'num_a1', 'num_a2', 'num_a3', 'num_a4', 'num_a5', 'O', 'O2', 'O3', 'O3S', 'OCLO', 'OCS', 'pom_a1', 'pom_a4', 'S', 'SF6', 'SO', 'SO2', 'SO3', 'so4_a1', 'so4_a2', 'so4_a3', 'so4_a5', 'soa_a1', 'soa_a2', 'SOAG', 'e', 'HO2', 'N2D', 'N2p', 'NOp', 'Np', 'O1D', 'O2_1D', 'O2_1S', 'O2p', 'OH', 'Op', 'Op2D', 'Op2P', 'H2O'), + }, +} diff --git a/mam4_jax/core/cam_topologies.py b/mam4_jax/core/cam_topologies.py new file mode 100644 index 0000000..3602fdf --- /dev/null +++ b/mam4_jax/core/cam_topologies.py @@ -0,0 +1,108 @@ +"""CAM mode topologies — GENERATED, do not hand-edit. + +Produced by `tools/dump_tables/to_topology.py` in the sibling repo +`mam-box-fortran`, from index tables read out of an initialised CAM MAM box +model. Those tables are not transcribable from source: `modal_aero_data.F90` +builds them at init from the chemistry preprocessor's species list. + +Regenerate with: + cd mam-box-fortran + ./build/build_cam.sh && ./build/build_cam.sh --mam5 + tools/dump_tables/run.sh mam4 > outputs/tables/cam_mam4_indices.py + tools/dump_tables/run.sh mam5 > outputs/tables/cam_mam5_indices.py + python3 tools/dump_tables/to_topology.py + +`lspectype_amode` here is SYNTHESISED: CAM has no such array, resolving each +(mode, slot) straight to its density and hygroscopicity. The generator derives +the type list from species-name prefixes and verifies it reproduces CAM's +per-slot arrays exactly; `tests/test_cam_topology.py` re-checks that from the +committed data, so the claim is not merely a generator-time assertion. +""" +from __future__ import annotations + +from mam4_jax.core.topology import Topology, register_topology + +# --- CAM MAM4 -------------------------------------------------------- +# source: cam_mam4_indices.py sha256: 1dd51e380a38ea35… +CAM_MAM4 = register_topology(Topology( + name="cam_mam4", + variant="cesm", + nmodes=4, + pcnst=31, + mode_names=('accum', 'aitken', 'coarse', 'primary_carbon'), + specname_amode=('so4', 'pom', 'soa', 'bc', 'dst', 'ncl'), + nspec_amode=(6, 4, 3, 2), + numptr_amode=(16, 17, 18, 19), + numptrcw_amode=(16, 17, 18, 19), + lspectype_amode=( + (0, 1, 2, 3, 4, 5), + (0, 2, 5, 4, -1, -1), + (4, 5, 0, -1, -1, -1), + (1, 3, -1, -1, -1, -1), + ), + lmassptr_amode=( + (23, 20, 26, 5, 8, 13), + (24, 27, 14, 9, -1, -1), + (10, 15, 25, -1, -1, -1), + (21, 6, -1, -1, -1, -1), + ), + lmassptrcw_amode=( + (23, 20, 26, 5, 8, 13), + (24, 27, 14, 9, -1, -1), + (10, 15, 25, -1, -1, -1), + (21, 6, -1, -1, -1, -1), + ), + specdens_amode=(1770.0, 1000.0, 1000.0, 1700.0, 2600.0, 1900.0), + spechygro_amode=(0.507, 1.000000082740371e-10, 0.14, 1.000000013351432e-10, 0.068, 1.16), + sigmag_amode=(1.8, 1.6, 1.8, 1.600000023841858), + dgnum_amode=(1.1e-07, 2.6e-08, 2e-06, 5.000000058430487e-08), + dgnumlo_amode=(5.35e-08, 8.7e-09, 1e-06, 9.99999993922529e-09), + dgnumhi_amode=(4.4e-07, 5.2e-08, 4e-06, 1.0000000116860974e-07), + rhcrystal_amode=(0.35, 0.35, 0.35, 0.35), + rhdeliques_amode=(0.8, 0.8, 0.8, 0.8), + provenance="CAM cam6_4_187, MAM4. Index tables and per-slot properties read out of an initialised box model " +)) + +# --- CAM MAM5 -------------------------------------------------------- +# source: cam_mam5_indices.py sha256: 9a4b4a28e7206bc7… +CAM_MAM5 = register_topology(Topology( + name="cam_mam5", + variant="cesm", + nmodes=5, + pcnst=108, + mode_names=('accum', 'aitken', 'coarse', 'primary_carbon', 'coarse_strat'), + specname_amode=('so4', 'pom', 'soa', 'bc', 'dst', 'ncl'), + nspec_amode=(6, 4, 3, 2, 1), + numptr_amode=(68, 69, 70, 71, 72), + numptrcw_amode=(68, 69, 70, 71, 72), + lspectype_amode=( + (0, 1, 2, 3, 4, 5), + (0, 2, 5, 4, -1, -1), + (4, 5, 0, -1, -1, -1), + (1, 3, -1, -1, -1, -1), + (0, -1, -1, -1, -1, -1), + ), + lmassptr_amode=( + (86, 79, 90, 5, 40, 62), + (87, 91, 63, 41, -1, -1), + (42, 64, 88, -1, -1, -1), + (80, 6, -1, -1, -1, -1), + (89, -1, -1, -1, -1, -1), + ), + lmassptrcw_amode=( + (86, 79, 90, 5, 40, 62), + (87, 91, 63, 41, -1, -1), + (42, 64, 88, -1, -1, -1), + (80, 6, -1, -1, -1, -1), + (89, -1, -1, -1, -1, -1), + ), + specdens_amode=(1770.0, 1000.0, 1000.0, 1700.0, 2600.0, 1900.0), + spechygro_amode=(0.507, 1.000000082740371e-10, 0.14, 1.000000013351432e-10, 0.068, 1.16), + sigmag_amode=(1.6, 1.6, 1.8, 1.600000023841858, 1.2), + dgnum_amode=(1.1e-07, 2.6e-08, 2e-06, 5.000000058430487e-08, 9e-07), + dgnumlo_amode=(5.35e-08, 8.7e-09, 1e-06, 9.99999993922529e-09, 4e-07), + dgnumhi_amode=(4.8e-07, 5.2e-08, 4e-06, 1.0000000116860974e-07, 4e-05), + rhcrystal_amode=(0.35, 0.35, 0.35, 0.35, 0.35), + rhdeliques_amode=(0.8, 0.8, 0.8, 0.8, 0.8), + provenance="CAM cam6_4_187, MAM5. Index tables and per-slot properties read out of an initialised box model " +)) diff --git a/mam4_jax/coupling/amicphys.py b/mam4_jax/coupling/amicphys.py index 0ab7180..530c83b 100644 --- a/mam4_jax/coupling/amicphys.py +++ b/mam4_jax/coupling/amicphys.py @@ -1003,6 +1003,7 @@ def amicphys(state: dict[str, Any], params: AmicphysParams | None = None, differently-configured instances in one process must use ``params``. """ del config + _check_clear_sky(state.get("cldn")) if params is None: params = AmicphysParams() return _mam_amicphys_1gridcell( @@ -1013,6 +1014,45 @@ def amicphys(state: dict[str, Any], params: AmicphysParams | None = None, ) +def _check_clear_sky(cldn) -> None: + """Refuse a non-zero cloud fraction, since the cloudy sub-area is not ported. + + Only the clear-sky sub-area is implemented. With ``cldn > 0`` the Fortran + splits the cell and area-weights two different sub-area calculations; this + port would instead apply clear-sky physics to the whole cell and return an + answer that looks fine. That is silent wrong physics, so it is refused. + + Checked here, at the public entry, rather than inside + ``_mam_amicphys_1gridcell``: under ``jax.jit`` the value is a tracer with no + readable magnitude, and a check that cannot fire is worse than no check + because it reads as protection. If ``cldn`` IS a tracer we say so instead of + pretending. An earlier version of this docstring claimed the error was + raised and no check existed at all. + """ + if cldn is None: + return + try: + worst = float(np.max(np.abs(np.asarray(cldn)))) + except (TypeError, ValueError, jax.errors.TracerArrayConversionError, + jax.errors.ConcretizationTypeError): + # Traced: no readable magnitude, so nothing can be checked here. Return + # SILENTLY rather than warning. driver.run_step is jitted, so the traced + # case is the normal one and a warning would fire on every single call -- + # and a warning that always fires gets filtered, at which point it + # protects nothing while still reading as protection. The real guard for + # that path runs before the jit, in driver.run_step / run_timesteps. + return + if worst > 0.0: + raise NotImplementedError( + f"amicphys: cloud fraction cldn has magnitude up to {worst:.3e}, but " + "only the clear-sky sub-area is ported. The Fortran splits the cell " + "and area-weights clear and cloudy calculations; applying clear-sky " + "physics to a partly cloudy cell would return a plausible but wrong " + "answer. Pass cldn = 0, or implement " + "_mam_amicphys_1subarea_cloudy." + ) + + def _mam_amicphys_1gridcell(state: dict[str, Any], params: AmicphysParams, *, mdo_gasaerexch: int, mdo_rename: int, @@ -1023,15 +1063,12 @@ def _mam_amicphys_1gridcell(state: dict[str, Any], The Fortran routine splits each grid cell into clear and cloudy sub-areas weighted by ``cldn``. For the canonical box-model setup ``cldn = 0`` everywhere (``driver.F90:591``), so only the clear-sky - path is exercised. The cloudy path is not implemented; calling this - with a non-zero cloud fraction in any cell raises a clear error so - future workflows don't silently get wrong physics. + path is exercised. The cloudy path is not implemented. + + The ``cldn`` guard lives in the public :func:`amicphys` entry, not here, + because by this point the value may be a tracer with no readable magnitude. + See :func:`_check_clear_sky`. """ - cldn = state.get("cldn") - # We don't enforce the cldn==0 check here because the value is a - # JAX array (could be traced); the box-model driver guarantees zero - # and our tests pass that explicitly. Cloudy support would land as a - # later PR alongside `_mam_amicphys_1subarea_cloudy`. return _mam_amicphys_1subarea_clear( state, params, mdo_gasaerexch=mdo_gasaerexch, mdo_rename=mdo_rename, @@ -1290,7 +1327,7 @@ def _mam_gasaerexch_1subarea(qgas, qaer, qnum, qwtr, def _mam_rename_1subarea(qnum_cur, qaer_cur, qaer_delsub_grow4rnam, - qwtr_cur, fac_m2v_aer): + qwtr_cur, fac_m2v_aer, *, method="e3sm"): """Port of ``mam_rename_1subarea`` (``modal_aero_amicphys.F90:3923–4246``). Operates on the amicphys-local single-(col, level, sub-area) view of @@ -1392,20 +1429,48 @@ def _mam_rename_1subarea(qnum_cur, qaer_cur, qaer_delsub_grow4rnam, tailfr_numnew = 0.5 * erfc(yn_tail_new) tailfr_volnew = 0.5 * erfc(yv_tail_new) - # Old tail fractions — with the optaa==40 dryvol/dgn adjustment. - # (Fortran lines 4135-4141.) + # Old tail fractions. THIS IS WHERE THE TWO ALGORITHMS DIVERGE. + # + # E3SM production runs rename_method_optaa = 40; CAM's default path + # (modal_aero_rename_no_acc_crs_sub) implements what that code calls the + # optaa /= 40 branch. They differ in exactly three decisions -- see + # mam-box-fortran/docs/reference/discrepancies/rename.md section 4: + # + # (1) whether the growth increment is gated BEFORE anything else, + # (2) what triggers the old-diameter clamp, and + # (3) whether the old VOLUME is rescaled along with the clamped diameter. dgn_t_old_raw = (dryvol_t_oldbnd / (num_t_oldbnd * factoraa_mfrm)) ** _ONETHIRD - above_cut = dgn_t_old_raw > dp_belowcut_mfrm - dryvol_t_old_used = jnp.where( - above_cut, - dryvol_t_old * (dp_belowcut_mfrm / dgn_t_old_raw) ** 3, - dryvol_t_old, - ) - dgn_t_old = jnp.where(above_cut, dp_belowcut_mfrm, dgn_t_old_raw) - # Guard 3 (Fortran line 4141, optaa==40 branch): - # (dryvol_t_new - dryvol_t_old_used) <= 1e-6 * dryvol_t_oldbnd. - guard_voldel = (dryvol_t_new - dryvol_t_old_used) > 1.0e-6 * dryvol_t_oldbnd + if method == "cam": + # CAM / E3SM-legacy. A1:479, 502-518 (identical to B:317, 340-356). + # (1) gate on the growth increment itself, up front + guard_voldel = dryvol_t_del > 1.0e-6 * dryvol_t_oldbnd + # (2) clamp fires on the NEW diameter reaching dp_cut, and clamps the + # diameter only -- via min(), so it never increases dgn_t_old + clamp = dgn_t_new >= dp_cut_mfrm + dgn_t_old = jnp.where(clamp, + jnp.minimum(dgn_t_old_raw, dp_belowcut_mfrm), + dgn_t_old_raw) + # (3) the old volume is NOT rescaled + dryvol_t_old_used = dryvol_t_old + elif method == "e3sm": + # optaa == 40. C:4108-4110, 4135-4141, 4156. + above_cut = dgn_t_old_raw > dp_belowcut_mfrm + dryvol_t_old_used = jnp.where( + above_cut, + dryvol_t_old * (dp_belowcut_mfrm / dgn_t_old_raw) ** 3, + dryvol_t_old, + ) + dgn_t_old = jnp.where(above_cut, dp_belowcut_mfrm, dgn_t_old_raw) + # The up-front growth gate is SKIPPED when optaa == 40; a different one + # is applied after the rescale instead (C:4141). + guard_voldel = (dryvol_t_new - dryvol_t_old_used) > 1.0e-6 * dryvol_t_oldbnd + else: + raise ValueError( + f"rename method must be 'cam' or 'e3sm', got {method!r}. " + "'cam' is modal_aero_rename_no_acc_crs_sub, which E3SM's code " + "calls its optaa /= 40 branch; 'e3sm' is optaa == 40." + ) lndgn_old = jnp.log(dgn_t_old) lndgv_old = lndgn_old + tmp_alnsg2_mfrm diff --git a/mam4_jax/coupling/cam_driver.py b/mam4_jax/coupling/cam_driver.py new file mode 100644 index 0000000..0857a96 --- /dev/null +++ b/mam4_jax/coupling/cam_driver.py @@ -0,0 +1,1104 @@ +"""CAM's process coupling — plan 024 PR G / plan 025 §7. + +CAM drives MAM microphysics as a SEQUENTIAL chain on grid-cell means +(``aero_model.F90:1202-1247``): ``modal_aero_gasaerexch_sub`` (which calls +rename internally) → ``modal_aero_newnuc_sub`` → ``modal_aero_coag_sub`` — +no sub-areas, no amicphys. This module ports that chain for the +**SO4-only box scope** (owner 2026-08-20: coagulation, condensation, +nucleation; no deposition, no transport, no organics evaporation). + +Everything here operates on the GAS-WINDOW view: arrays of shape +``(..., gas_pcnst)`` holding volume mixing ratios (mol/mol for mass, +#/kmol-air for number) — exactly what CAM passes (``vmr``, +aero_model.F90:1202) and what the sibling-repo box driver hands to +``mam_microphysics_cam``. The mmr↔vmr boundary conversion belongs to the +driver-assembly step (plan 025 G4), not here. + +Topology-threading: this module is the first real consumer of the +``Topology`` axis. Every mode/species table is resolved from a +``Topology`` instance plus the generated ``cam_params`` layer through +:func:`_cam_tables` (cached per topology name, plain numpy — safe to read +at trace time because the TOPOLOGY IS AN ARGUMENT, never a module-global +read inside a kernel; see core/topology.py's staleness guard). + +SO4-only reductions, each exact for the scope rather than approximate: + +* NH3/MSA: absent from the chemistry mechanism used (`do_nh4g`/`do_msag` + false paths). +* SOA: the mechanism HAS soa/SOAG tracers, but the SO4-only scenarios hold + them identically zero, and zero gas + zero aerosol is a fixed point of + ``modal_aero_soaexch`` — assumption **A13**, verified empirically by the + capture-parity tests (the capture runs the FULL Fortran subroutine). +* Cloud-borne (qqcw) tracers: identically zero (``cldfr = 0`` box), so the + qqcw half of rename is a no-op and is not carried. +* Diagnostics (``qsrflx``, ``dotend``, outfld) are not carried; tendencies + are applied densely (adding an exact 0.0 tendency is the identity). + +Faithfulness notes: + +* ``1 - exp(-x)`` is written ``-expm1(-x)`` (repo standard, plan 026 / + ADR-019; worth ~1e-11 relative near thresholds, nothing elsewhere). +* The legacy primary-carbon aging block INSIDE gasaerexch + (modal_aero_gasaerexch.F90:719-806) ages at + ``n_so4_monolayers_pcage = 8.0`` — the gasaerexch module's own + ``parameter`` (:37). This is a different code line from amicphys' + phys_control-fed 3.0 and is ported as CAM has it, NOT shared with the + E3SM path's ``configure_pcarbon_aging``. +* CAM's ``gas_aer_uptkrates`` is ported as its own function — it is a + THIRD variant (fixed ``beta = 2``, hardcoded ac = 0.65 literals, + truncated ``tworootpi``/``root2``), not the amicphys quadrature already + in ``coupling/amicphys.py``. See plan 025 §7. +""" +from __future__ import annotations + +import functools + +import jax.numpy as jnp +import numpy as np + +from mam4_jax.core.cam_params import CAM_PARAMS +from mam4_jax.core.topology import Topology, get_topology +from mam4_jax.physics.strat_sulfate import h2so4_reversible_uptake + +__all__ = [ + "cam_run_step", + "cam_run_timesteps", + "gas_aer_uptkrates_cam", + "mam_microphysics_cam", + "modal_aero_coag_cam", + "modal_aero_gasaerexch_cam", + "modal_aero_newnuc_cam", +] + +# CAM physconst constants, spelled EXACTLY as shr_const_mod computes them: +# SHR_CONST_RGAS = AVOGAD * BOLTZ = 8314.467591 J/K/kmol — NOT the rounded +# 8.31446e3 (that shortcut is 9.1e-7 relative off, which the implicit +# coagulation number solves amplify to ~2e-6; found by capture parity). +_RGAS_UNIV = 6.02214e26 * 1.38065e-23 # J/K/kmol (shr_const_rgas) +_MWDAIR = 28.966 # kg/kmol (shr_const_mwdair) +_RAIR = _RGAS_UNIV / _MWDAIR + +#: gasaerexch's own aging threshold (modal_aero_gasaerexch.F90:37-44): +#: a Fortran ``parameter`` — the legacy code line's value, NOT the +#: amicphys/phys_control 3.0. Deliberately not configurable here. +_N_SO4_MONOLAYERS_PCAGE = 8.0 +_DR_SO4_MONOLAYERS_PCAGE = _N_SO4_MONOLAYERS_PCAGE * 4.76e-10 + + +class _CamTables: + """Static per-topology tables for the CAM chain, gas-window indexed. + + Plain numpy / Python ints, built once per topology (cached). All + tracer indices are 0-based GAS-WINDOW indices (pcnst index − loffset); + ``-1`` marks an absent slot. + """ + + def __init__(self, topology: Topology): + p = CAM_PARAMS[topology.name] + names = p["cnst_names"] + off = p["loffset"] + nm = topology.nmodes + self.topology = topology + self.gas_pcnst = p["gas_pcnst"] + self.loffset = off + self.mwdry = p["mwdry"] + self.adv_mass = np.asarray(p["adv_mass"]) + self.cnst_names = names + + self.l_h2so4 = names.index("H2SO4") + self.l_so2 = names.index("SO2") if "SO2" in names else -1 + + # Mode-indexed tables (gas-window indices). + self.num_ptr = np.asarray( + [topology.numptr_amode[m] - off for m in range(nm)]) + self.lmass = [ + [topology.lmassptr_amode[m][s] - off + for s in range(topology.nspec_amode[m])] + for m in range(nm) + ] + # fac_m2v per (mode, slot): specmw/specdens, (m3-AP/kmol-AP). + mw = p["specmw_amode"] + dens = topology.specdens_amode + self.fac_m2v = [ + [mw[t] / dens[t] for t in topology.lspectype_amode[m][ + :topology.nspec_amode[m]]] + for m in range(nm) + ] + + # so4 per mode: window index of the mode's so4 tracer, else -1. + so4_type = topology.specname_amode.index("so4") + self.lptr_so4 = np.full(nm, -1, dtype=int) + for m in range(nm): + for s in range(topology.nspec_amode[m]): + if topology.lspectype_amode[m][s] == so4_type: + self.lptr_so4[m] = topology.lmassptr_amode[m][s] - off + self.fac_m2v_so4 = mw[so4_type] / dens[so4_type] + + # ido_so4a (gasaerexch_init:303-345): 1 = mode carries so4; + # 2 = the aging source mode (pcarbon); 0 = inactive. + self.mode_pcarbon = (topology.mode_index("primary_carbon") + if topology.has_mode("primary_carbon") else -1) + self.mode_accum = topology.mode_index("accum") + self.mode_aitken = topology.mode_index("aitken") + self.ido_so4a = np.where(self.lptr_so4 >= 0, 1, 0) + if self.mode_pcarbon >= 0 and self.lptr_so4[self.mode_accum] >= 0: + self.ido_so4a[self.mode_pcarbon] = 2 + + # Primary-carbon aging pair list (gasaerexch_init: number first, + # then each pcarbon species matched to the accum species of the + # same name prefix; aerosol water skipped). (from, to) window + # indices; to = -1 when no counterpart exists. + self.pcage_pairs: list[tuple[int, int]] = [] + if self.mode_pcarbon >= 0 and self.ido_so4a[self.mode_pcarbon] == 2: + mf, mt = self.mode_pcarbon, self.mode_accum + self.pcage_pairs.append( + (int(self.num_ptr[mf]), int(self.num_ptr[mt]))) + for s in range(topology.nspec_amode[mf]): + lf = topology.lmassptr_amode[mf][s] - off + prefix = names[lf].rsplit("_", 1)[0] + lt = -1 + for s2 in range(topology.nspec_amode[mt]): + cand = topology.lmassptr_amode[mt][s2] - off + if names[cand].rsplit("_", 1)[0] == prefix: + lt = cand + break + self.pcage_pairs.append((lf, lt)) + alnsg = np.log(np.asarray(topology.sigmag_amode)) + self.alnsg = alnsg + self.sigmag = np.asarray(topology.sigmag_amode) + if self.mode_pcarbon >= 0: + self.fac_volsfc_pcarbon = float( + np.exp(2.5 * alnsg[self.mode_pcarbon] ** 2)) + self.fac_m2v_pcarbon = np.asarray( + self.fac_m2v[self.mode_pcarbon]) + + # Rename pair (A1, acc_crs off): aitken -> accum only + # (rename_init). Species list: NUMBER FIRST (iq=1 moves by + # xferfrac_num), then each aitken species matched to accum by + # name prefix (all four match in both topologies). + mf, mt = self.mode_aitken, self.mode_accum + self.rename_pairs: list[tuple[int, int]] = [ + (int(self.num_ptr[mf]), int(self.num_ptr[mt]))] + for s in range(topology.nspec_amode[mf]): + lf = topology.lmassptr_amode[mf][s] - off + prefix = names[lf].rsplit("_", 1)[0] + lt = -1 + for s2 in range(topology.nspec_amode[mt]): + cand = topology.lmassptr_amode[mt][s2] - off + if names[cand].rsplit("_", 1)[0] == prefix: + lt = cand + break + self.rename_pairs.append((lf, lt)) + # Rename-from dry-volume ingredients: (window index, fac_m2v) per + # aitken slot. + self.rename_frm_slots = [ + (topology.lmassptr_amode[mf][s] - off, self.fac_m2v[mf][s]) + for s in range(topology.nspec_amode[mf]) + ] + + # Coagulation pair species lists (coag_init:800-870, name-matched + # against the EFFECTIVE destination = accum for all three pairs). + # Pair 3 (ait->pca, effective accum) carries the same (from, to) + # species list as pair 1, so only two lists are needed; what pair + # 3 adds is fac_m2v_aitage (init:906-955): so4 at face value, soa + # scaled by its equivalent-so4 hygroscopicity factor + # (spechygro_soa / spechygro_so4, gasaerexch_init:1861), every + # other species contributing ZERO shell volume. + def _match(mfrm, mtoo): + pairs = [] + for s_ in range(topology.nspec_amode[mfrm]): + lf_ = topology.lmassptr_amode[mfrm][s_] - off + pre = names[lf_].rsplit("_", 1)[0] + lt_ = -1 + for s2_ in range(topology.nspec_amode[mtoo]): + cand_ = topology.lmassptr_amode[mtoo][s2_] - off + if names[cand_].rsplit("_", 1)[0] == pre: + lt_ = cand_ + break + pairs.append((lf_, lt_)) + return pairs + + self.coag_ait_pairs = _match(self.mode_aitken, self.mode_accum) + self.coag_pca_pairs = _match(self.mode_pcarbon, self.mode_accum) \ + if self.mode_pcarbon >= 0 else [] + so4_t = topology.specname_amode.index("so4") + soa_t = (topology.specname_amode.index("soa") + if "soa" in topology.specname_amode else -1) + hygro = topology.spechygro_amode + self.fac_m2v_aitage = [] + for s_ in range(topology.nspec_amode[self.mode_aitken]): + t_ = topology.lspectype_amode[self.mode_aitken][s_] + if t_ == so4_t: + self.fac_m2v_aitage.append(self.fac_m2v[self.mode_aitken][s_]) + elif t_ == soa_t: + self.fac_m2v_aitage.append( + (hygro[soa_t] / hygro[so4_t]) + * self.fac_m2v[self.mode_aitken][s_]) + else: + self.fac_m2v_aitage.append(0.0) + + +@functools.lru_cache(maxsize=8) +def _cam_tables_by_name(name: str) -> _CamTables: + from mam4_jax.core import topology as topo_mod + try: + return _CamTables(topo_mod._REGISTRY[name]) # noqa: SLF001 + except KeyError: + raise KeyError(f"no registered topology named {name!r}") from None + + +def _cam_tables(topology: Topology | None) -> _CamTables: + if topology is None: + topology = get_topology() + return _cam_tables_by_name(topology.name) + + +# --------------------------------------------------------------------------- +# gas_aer_uptkrates — CAM's variant (modal_aero_gasaerexch.F90:953-1086) +# --------------------------------------------------------------------------- + +# CAM's own truncated literals — ported verbatim, NOT replaced with exact +# sqrt(pi)/sqrt(2) (the amicphys port uses exact values; this variant's +# reference is CAM, and normalising them changes answers at ~1e-8). +_TWOROOTPI_CAM = 3.5449077 +_ROOT2_CAM = 1.4142135 +_BETA_CAM = 2.0 +_XGHQ_CAM = (0.70710678, -0.70710678) +_WGHQ_CAM = (0.88622693, 0.88622693) + + +def gas_aer_uptkrates_cam(qnum, t, pmid, dgncur_awet, sigmag): + """H2SO4 gas-to-aerosol uptake rate per mode (1/s) — CAM's variant. + + Port of ``gas_aer_uptkrates`` (modal_aero_gasaerexch.F90:953-1086): + two-point Gauss-Hermite quadrature of ``2*pi*D*Dp*F(Kn, ac)`` over the + log-normal, with **fixed** ``beta = 2`` (the amicphys variant computes + a Knudsen-dependent beta), hardcoded ac = 0.65 Fuchs-Sutugin literals + (``0.4875 = 0.75*0.65``, ``1.184 = 1 + 0.283*0.65``), CAM's own + ``gasdiffus = 0.557e-4 * T**1.75 / p`` and + ``gasspeed = 14.70 * sqrt(T)``, and the truncated + ``tworootpi``/``root2``/quadrature literals above. + + Parameters + ---------- + qnum : (..., nmodes) — mode number mixing ratios (#/kmol-air). + t, pmid : (...,) — temperature (K), pressure (Pa). + dgncur_awet : (..., nmodes) — wet number-median diameters (m). + sigmag : (nmodes,) — geometric standard deviations (static). + + Returns ``uptkrate`` with shape (..., nmodes). + """ + t = jnp.asarray(t)[..., None] + pmid = jnp.asarray(pmid)[..., None] + rhoair = pmid / (_RAIR * t) # kg/m3 + aircon = rhoair / _MWDAIR # kmol-air/m3 + num_a = qnum * aircon # #/m3 + + gasdiffus = 0.557e-4 * t ** 1.75 / pmid # m2/s + gasspeed = 1.470e1 * jnp.sqrt(t) # m/s + freepathx2 = 6.0 * gasdiffus / gasspeed # m + + lnsg = jnp.log(jnp.asarray(sigmag)) # (nmodes,) + lndpgn = jnp.log(dgncur_awet) + const = _TWOROOTPI_CAM * num_a * jnp.exp( + _BETA_CAM * lndpgn + 0.5 * (_BETA_CAM * lnsg) ** 2) + + sumghq = jnp.zeros_like(dgncur_awet) + for xq, wq in zip(_XGHQ_CAM, _WGHQ_CAM): + lndp = lndpgn + _BETA_CAM * lnsg ** 2 + _ROOT2_CAM * lnsg * xq + dp = jnp.exp(lndp) + knudsen = freepathx2 / dp + fuchs_sutugin = (0.4875 * (1.0 + knudsen)) / ( + knudsen * (1.184 + knudsen) + 0.4875) + sumghq = sumghq + wq * dp * fuchs_sutugin / dp ** _BETA_CAM + + return const * gasdiffus * sumghq + + +# --------------------------------------------------------------------------- +# rename A1 — modal_aero_rename_no_acc_crs_sub (modal_aero_rename.F90:243-624) +# --------------------------------------------------------------------------- + +_FRELAX = 27.0 +_DRYVOL_SMALLEST = 1.0e-25 + + +def _rename_no_acc_crs_cam(q, dqdt, deltat, tables: _CamTables): + """CAM's default rename (A1), interstitial half, single pair. + + Adds the aitken → accum renaming tendencies onto ``dqdt`` and returns + it. ``q`` is the PRE-growth state; the incoming ``dqdt`` carries the + continuous-growth (condensation + aging) tendencies, exactly as the + Fortran receives them. ``dqdt_other`` and the cloud-borne half are + identically zero in the box scope and not carried. + + The Fortran's per-(i,k) early ``cycle``s become ``where`` masks: a + cell that fails a guard contributes an exact 0.0 tendency. + """ + topo = tables.topology + mf, mt = tables.mode_aitken, tables.mode_accum + alnsg_f = float(tables.alnsg[mf]) + alnsg_t = float(tables.alnsg[mt]) + dgnum_f = topo.dgnum_amode[mf] + + deltatinv = 1.0 / (deltat * (1.0 + 1.0e-15)) + xferfrac_max = 1.0 - 10.0 * float(jnp.finfo(jnp.float64).eps) + + factoraa = (np.pi / 6.0) * np.exp(4.5 * alnsg_f ** 2) + factoryy = np.sqrt(0.5) / alnsg_f + v2nlorlx = topo.voltonumblo_amode[mf] * _FRELAX + v2nhirlx = topo.voltonumbhi_amode[mf] / _FRELAX + dum3alnsg2 = 3.0 * alnsg_f ** 2 + dp_cut = np.sqrt( + topo.dgnum_amode[mf] * np.exp(1.5 * alnsg_f ** 2) + * topo.dgnum_amode[mt] * np.exp(1.5 * alnsg_t ** 2)) + lndp_cut = np.log(dp_cut) + dp_belowcut = 0.99 * dp_cut + + # Dry volume of the "from" mode and its growth increment, from ALL of + # the mode's species (dqdt_other = 0 in scope). + dryvol_t_old = jnp.zeros(q.shape[:-1], dtype=q.dtype) + dryvol_t_del = jnp.zeros(q.shape[:-1], dtype=q.dtype) + for lw, m2v in tables.rename_frm_slots: + dryvol_t_old = dryvol_t_old + m2v * jnp.maximum(0.0, q[..., lw]) + dryvol_t_del = dryvol_t_del + (m2v * deltat) * dqdt[..., lw] + dryvol_t_new = dryvol_t_old + dryvol_t_del + dryvol_t_oldbnd = jnp.maximum(dryvol_t_old, _DRYVOL_SMALLEST) + + ok = dryvol_t_new > _DRYVOL_SMALLEST + ok = ok & (dryvol_t_del > 1.0e-6 * dryvol_t_oldbnd) + + num_t_old = jnp.maximum(0.0, q[..., tables.num_ptr[mf]]) + num_t_oldbnd = jnp.minimum(dryvol_t_oldbnd * v2nlorlx, num_t_old) + num_t_oldbnd = jnp.maximum(dryvol_t_oldbnd * v2nhirlx, num_t_oldbnd) + + dgn_t_new = (dryvol_t_new / (num_t_oldbnd * factoraa)) ** (1.0 / 3.0) + ok = ok & (dgn_t_new > dgnum_f) + + from jax.scipy.special import erfc + + lndgn_new = jnp.log(dgn_t_new) + lndgv_new = lndgn_new + dum3alnsg2 + tailfr_numnew = 0.5 * erfc((lndp_cut - lndgn_new) * factoryy) + tailfr_volnew = 0.5 * erfc((lndp_cut - lndgv_new) * factoryy) + + dgn_t_old = (dryvol_t_oldbnd / (num_t_oldbnd * factoraa)) ** (1.0 / 3.0) + dgn_t_old = jnp.where(dgn_t_new >= dp_cut, + jnp.minimum(dgn_t_old, dp_belowcut), dgn_t_old) + lndgn_old = jnp.log(dgn_t_old) + lndgv_old = lndgn_old + dum3alnsg2 + tailfr_numold = 0.5 * erfc((lndp_cut - lndgn_old) * factoryy) + tailfr_volold = 0.5 * erfc((lndp_cut - lndgv_old) * factoryy) + + dum = tailfr_volnew * dryvol_t_new - tailfr_volold * dryvol_t_old + ok = ok & (dum > 0.0) + + safe_new = jnp.where(ok, dryvol_t_new, 1.0) + xferfrac_vol = jnp.minimum(dum, safe_new) / safe_new + xferfrac_vol = jnp.minimum(xferfrac_vol, xferfrac_max) + xferfrac_num = tailfr_numnew - tailfr_numold + xferfrac_num = jnp.maximum(0.0, jnp.minimum(xferfrac_num, xferfrac_vol)) + xferfrac_vol = jnp.where(ok, xferfrac_vol, 0.0) + xferfrac_num = jnp.where(ok, xferfrac_num, 0.0) + + for iq, (lf, lt) in enumerate(tables.rename_pairs): + xfercoef = (xferfrac_num if iq == 0 else xferfrac_vol) * deltatinv + xfertend = xfercoef * jnp.maximum( + 0.0, q[..., lf] + dqdt[..., lf] * deltat) + dqdt = dqdt.at[..., lf].add(-xfertend) + if lt >= 0: + dqdt = dqdt.at[..., lt].add(xfertend) + return dqdt + + +# --------------------------------------------------------------------------- +# gasaerexch — modal_aero_gasaerexch_sub, SO4-only +# --------------------------------------------------------------------------- + +def modal_aero_gasaerexch_cam(q, t, pmid, deltat, dgncur_a, dgncur_awet, + *, topology=None, sulfeq=None): + """One gasaerexch call on the gas window — CAM's SO4-only chain. + + Port of ``modal_aero_gasaerexch_sub`` (modal_aero_gasaerexch.F90), + reduced exactly to the SO4-only box scope (module docstring): + + 1. per-mode uptake rates (:func:`gas_aer_uptkrates_cam`); + 2. H2SO4 condensation — irreversible ``fgain``-split when ``sulfeq`` + is None (tropospheric), or the reversible sulfeq-limited solve + (stratospheric; ``k <= troplev`` everywhere in the box); + 3. the legacy primary-carbon aging block at 8.0 monolayers + (:719-806) — this-step condensed shell only; + 4. rename A1 (aitken → accum), fed the accumulated ``dqdt``; + 5. ``q += dqdt * deltat``. + + Parameters + ---------- + q : (..., gas_pcnst) — VOLUME mixing ratios (mol/mol, #/kmol-air). + t, pmid : (...,); deltat : scalar (s). + dgncur_a, dgncur_awet : (..., nmodes) — dry / wet mode diameters (m). + topology : static ``Topology`` (None → active topology). + sulfeq : None for the tropospheric path, else (..., nmodes) + equilibrium H2SO4 over each mode (mol/mol) from + :func:`mam4_jax.physics.strat_sulfate.calc_h2so4_equilib_mixrat`. + + Returns the updated ``q``. + """ + tb = _cam_tables(topology) + deltatxx = deltat * (1.0 + 1.0e-15) + + qnum = q[..., tb.num_ptr] # (..., nmodes) + uptkrate = gas_aer_uptkrates_cam(qnum, t, pmid, dgncur_awet, tb.sigmag) + + active = jnp.asarray(tb.ido_so4a > 0) + uptk = jnp.where(active, uptkrate, 0.0) + sum_uprt_so4 = jnp.sum(uptk, axis=-1) + + qgas = q[..., tb.l_h2so4] + + if sulfeq is None: + # Tropospheric: irreversible uptake, fgain split (:492-575). + safe_sum = jnp.where(sum_uprt_so4 > 0.0, sum_uprt_so4, 1.0) + fgain = jnp.where(sum_uprt_so4[..., None] > 0.0, + uptk / safe_sum[..., None], 0.0) + avg_uprt = -jnp.expm1(-deltatxx * sum_uprt_so4) / deltatxx + sum_dqdt_so4 = qgas * avg_uprt + dqdt_so4 = fgain * sum_dqdt_so4[..., None] # (..., nmodes) + sum_dqdt_out = sum_dqdt_so4 + else: + # Stratospheric: reversible, sulfeq-limited (:523-566). + qaer_so4 = jnp.stack( + [q[..., tb.lptr_so4[m]] if tb.lptr_so4[m] >= 0 + else jnp.zeros_like(qgas) + for m in range(tb.topology.nmodes)], axis=-1) + dqdt_so4, sum_dqdt_out = h2so4_reversible_uptake( + qgas, qaer_so4, uptkrate, sulfeq, deltat, + jnp.asarray(tb.ido_so4a)) + + # Assemble dqdt on the window: so4 slots (ido == 1) and the gas. + dqdt = jnp.zeros_like(q) + for m in range(tb.topology.nmodes): + if tb.ido_so4a[m] == 1: + dqdt = dqdt.at[..., tb.lptr_so4[m]].set(dqdt_so4[..., m]) + dqdt = dqdt.at[..., tb.l_h2so4].set(-sum_dqdt_out) + + # Legacy primary-carbon aging (:719-806). SO4-only: the shell is this + # step's condensed so4 on the pcarbon mode; nh4/soa terms absent. + if tb.mode_pcarbon >= 0 and tb.ido_so4a[tb.mode_pcarbon] == 2: + mp = tb.mode_pcarbon + vol_shell = deltat * dqdt_so4[..., mp] * tb.fac_m2v_so4 + vol_core = jnp.zeros_like(vol_shell) + for s, lw in enumerate(tb.lmass[mp]): + vol_core = vol_core + q[..., lw] * tb.fac_m2v_pcarbon[s] + tmp1 = vol_shell * dgncur_a[..., mp] * tb.fac_volsfc_pcarbon + tmp2 = jnp.maximum(6.0 * _DR_SO4_MONOLAYERS_PCAGE * vol_core, 0.0) + xferfrac_max = 1.0 - 10.0 * float(jnp.finfo(jnp.float64).eps) + saturated = tmp1 >= tmp2 + safe_tmp2 = jnp.where(saturated, 1.0, tmp2) + xferfrac = jnp.where(saturated, xferfrac_max, + jnp.minimum(tmp1 / safe_tmp2, xferfrac_max)) + fire = xferfrac > 0.0 + rate = jnp.where(fire, xferfrac, 0.0) / deltat + for lf, lt in tb.pcage_pairs: + xferrate = rate * q[..., lf] + dqdt = dqdt.at[..., lf].add(-xferrate) + if lt >= 0: + dqdt = dqdt.at[..., lt].add(xferrate) + # Condensed-on-pcarbon so4 lands on accum's so4 slot — but ONLY + # when the aging fires (:770): with xferfrac == 0 CAM drops it. + if tb.ido_so4a[tb.mode_accum] > 0: + dqdt = dqdt.at[..., tb.lptr_so4[tb.mode_accum]].add( + jnp.where(fire, dqdt_so4[..., mp], 0.0)) + + # Rename A1 (aitken -> accum), then apply everything (:806-838). + dqdt = _rename_no_acc_crs_cam(q, dqdt, deltat, tb) + return q + dqdt * deltat + + +# --------------------------------------------------------------------------- +# newnuc — modal_aero_newnuc_sub (modal_aero_newnuc.F90:59-520) +# --------------------------------------------------------------------------- + +#: skip nucleation entirely below this H2SO4 vmr (newnuc.F90:30). +_QH2SO4_CUTOFF = 4.0e-16 + + +def modal_aero_newnuc_cam(q, t, pmid, deltat, qv, zm, pblh, + del_h2so4_gasprod, del_h2so4_aeruptk, + *, topology=None): + """One newnuc call on the gas window — CAM's wrapper, SO4-only. + + Port of ``modal_aero_newnuc_sub`` around the already-ported + ``mer07_veh02_nuc_mosaic_1box`` dispatcher (the leaf + parameterizations are 0-diff between CAM and E3SM; the WRAPPER is + CAM-specific). What the wrapper owns: + + * the reconstruction of the step-average H2SO4 from + ``del_h2so4_gasprod`` (gas-phase production over the step) and + ``del_h2so4_aeruptk`` (loss to condensation over the step, <= 0): + ``tmp_q2 = q3 + max(0, -aeruptk)`` is the pre-uptake gas, + ``tmpb = log(q2/q3)`` (clamped to 20, with q3 clamped up to + ``q2*exp(-20)``) gives the uptake rate, and the average follows the + production-during-decay closed form (:262-292); + * relative humidity through CAM's TABLE ``qsat`` + (:mod:`mam4_jax.physics.cam_saturation`) — mixed-phase, NOT the + direct over-water formula; + * the two H2SO4 cutoffs (4e-16 on current AND average), the + 100 #/kmol-air/s rate floor, and the grown-particle size + constraints against the aitken lo/hi single-particle masses; + * tendencies onto (H2SO4, so4_aitken, num_aitken). ``cld = 0`` in + the box scope, so the ``(1-cldx)`` weights are 1 and the + ``cld >= 0.99`` skip never fires; NH3 is absent. + + Every Fortran ``cycle`` becomes a mask; dispatcher inputs are + clamped to benign values on masked cells (double-where) so no dead + branch poisons reverse-mode. + + Returns the updated ``q``. + """ + from mam4_jax.physics.cam_saturation import qsat_cam + from mam4_jax.physics.newnuc import mer07_veh02_nuc_mosaic_1box + + tb = _cam_tables(topology) + topo = tb.topology + mait = tb.mode_aitken + lnum = int(tb.num_ptr[mait]) + lso4 = int(tb.lptr_so4[mait]) + mw_so4 = CAM_PARAMS[topo.name]["specmw_amode"][ + topo.specname_amode.index("so4")] + dens_so4 = topo.specdens_amode[topo.specname_amode.index("so4")] + + # Grown-particle dry-diameter window and single-particle masses. + dplom = float(np.exp(0.67 * np.log(topo.dgnumlo_amode[mait]) + + 0.33 * np.log(topo.dgnum_amode[mait]))) + dphim = topo.dgnumhi_amode[mait] + mass1p_aitlo = dens_so4 * np.pi / 6.0 * dplom ** 3 + mass1p_aithi = dens_so4 * np.pi / 6.0 * dphim ** 3 + + qh2so4_cur = q[..., tb.l_h2so4] + go = qh2so4_cur > _QH2SO4_CUTOFF + + # Step-average H2SO4 reconstruction (:262-292). + tmpa = jnp.maximum(0.0, del_h2so4_gasprod) + tmp_q3 = qh2so4_cur + tmp_q2 = tmp_q3 + jnp.maximum(0.0, -del_h2so4_aeruptk) + tmpc = tmp_q2 * np.exp(-20.0) + no_uptake = tmp_q2 <= tmp_q3 + clamped = (~no_uptake) & (tmp_q3 <= tmpc) + q3_eff = jnp.where(clamped, tmpc, tmp_q3) + safe_ratio = jnp.where(no_uptake | clamped, 1.0, tmp_q2 / + jnp.where(q3_eff > 0.0, q3_eff, 1.0)) + tmpb = jnp.where(no_uptake, 0.0, + jnp.where(clamped, 20.0, jnp.log(safe_ratio))) + tmp_uptkrate = tmpb / deltat + + small = tmpb <= 0.1 + safe_tmpb = jnp.where(small, 1.0, tmpb) + tmpc2 = tmpa / safe_tmpb + avg_big = (q3_eff - tmpc2) * (jnp.expm1(safe_tmpb) / safe_tmpb) + tmpc2 + avg_small = q3_eff * (1.0 + 0.5 * tmpb) - 0.5 * tmpa + qh2so4_avg = jnp.where(small, avg_small, avg_big) + go = go & (qh2so4_avg > _QH2SO4_CUTOFF) + + # RH via the TABLE qsat; cld = 0 so grid-average == clear-sky. + _es, qs = qsat_cam(t, pmid) + qvswtr = jnp.maximum(qs, 1.0e-20) + relhum = jnp.clip(qv / qvswtr, 0.0, 1.0) + relhumnn = jnp.clip(relhum, 0.01, 0.99) + + # Dispatcher, on benign inputs where masked. + safe_cur = jnp.where(go, qh2so4_cur, 1.0e-14) + safe_avg = jnp.where(go, qh2so4_avg, 1.0e-14) + (_isize, qnuma_del, qso4a_del, _qnh4a_del, _qh2so4_del, _qnh3_del, + _dens, _dncl) = mer07_veh02_nuc_mosaic_1box( + dtnuc=deltat, temp=t, rh=relhumnn, press=pmid, zm=zm, pblh=pblh, + qh2so4_cur=safe_cur, qh2so4_avg=safe_avg, + h2so4_uptkrate=tmp_uptkrate, + dplom_sect=dplom, dphim_sect=dphim, + newnuc_method_flagaa=11, mw_so4a_host=mw_so4) + + # (#/mol-air) -> (#/kmol-air); rates; SO4-only mass fraction = 1. + qnuma_del = jnp.where(go, qnuma_del, 0.0) * 1.0e3 + qso4a_del = jnp.where(go, qso4a_del, 0.0) + dndt = qnuma_del / deltat + tmpa_m = qso4a_del * mw_so4 + tmp_frso4 = jnp.maximum(tmpa_m, 1.0e-35) / jnp.maximum(tmpa_m, 1.0e-35) + dmdt = jnp.maximum(0.0, tmpa_m / deltat) + + # Rate floor (:404) then size constraints (:415-428). + live = dndt >= 1.0e2 + dndt = jnp.where(live, dndt, 0.0) + dmdt = jnp.where(live, dmdt, 0.0) + safe_dndt = jnp.where(live, dndt, 1.0) + mass1p = jnp.where(live, dmdt / safe_dndt, mass1p_aitlo) + dndt = jnp.where(mass1p < mass1p_aitlo, dmdt / mass1p_aitlo, dndt) + dmdt = jnp.where(mass1p > mass1p_aithi, dndt * mass1p_aithi, dmdt) + + dso4dt = dmdt * tmp_frso4 / mw_so4 + q = q.at[..., tb.l_h2so4].add(-dso4dt * deltat) + q = q.at[..., lso4].add(dso4dt * deltat) + q = q.at[..., lnum].add(dndt * deltat) + return q + + +# --------------------------------------------------------------------------- +# coag — modal_aero_coag_sub, pair_option_acoag == 3 +# (modal_aero_coag.F90:73-709; init tables :714-990) +# --------------------------------------------------------------------------- + +def _coag_number_new(tmpn, tmpa, tmpb): + """The three-branch closed form for a mode's number after ``deltat`` + of intermodal (rate ``tmpa/deltat``) plus self (coefficient + ``tmpb/deltat``) coagulation loss (modal_aero_coag.F90:459-471, + faithful branch thresholds |tmpc| < 0.01, |tmpa| < 0.001). + + Every branch is evaluated on guarded operands (double-where) so no + dead branch poisons reverse-mode. + """ + tmpc = tmpa + tmpb * tmpn + b_small_c = jnp.abs(tmpc) < 0.01 + b_small_a = jnp.abs(tmpa) < 0.001 + + n_small_c = tmpn * jnp.exp(-tmpc) + n_small_a = jnp.exp(-tmpa) * tmpn / (1.0 + tmpb * tmpn) + + safe_tmpc = jnp.where(jnp.abs(tmpc) > 0.0, tmpc, 1.0) + tmpf = tmpb * tmpn / safe_tmpc + tmpg = jnp.exp(-tmpa) + den = 1.0 - tmpg * tmpf + safe_den = jnp.where(jnp.abs(den) > 0.0, den, 1.0) + tmph = tmpg * (1.0 - tmpf) / safe_den + n_general = tmpn * jnp.maximum(0.0, jnp.minimum(1.0, tmph)) + + return jnp.where(b_small_c, n_small_c, + jnp.where(b_small_a, n_small_a, n_general)) + + +def modal_aero_coag_cam(q, t, pmid, deltat, dgncur_a, dgncur_awet, + wetdens_a, *, topology=None): + """One coag call on the gas window — CAM's ``pair_option_acoag = 3``. + + Port of ``modal_aero_coag_sub``: three pairs (aitken→accum, + pcarbon→accum, aitken→pcarbon-effective-accum) with Whitby fast + coefficients from the byte-identical (and already-ported) + ``getcoags_wrapper_f``, then: + + 1. number: accum self-coag (``n/(1+Δt·βjj0·n)``), then pcarbon and + aitken via the three-branch closed form + (:func:`_coag_number_new`), each consuming the PRIOR mode's + time-average number — sequencing is load-bearing; + 2. aitken mass: one transfer at the COMBINED loss + ``βij3(ait,acc)·n̄acc + βij3(ait,pca)·n̄pca``, all of it delivered + to the ACCUM species (the pcarbon-destined share is deemed aged + through); that share × ``fac_m2v_aitage`` accumulates the aging + SHELL volume (so4 at face value, soa at its equivalent-so4 + hygroscopicity factor, ncl/dst contributing zero — init:906-955); + 3. the aging fraction from shell vs core against the same legacy + 8.0-monolayer criterion as gasaerexch (the Fortran comment says + "this duplicates the code in modal_aero_gasaerexch"); + 4. pcarbon mass and number: direct coagulation PLUS the aging + fraction, capped at ``1 − 10ε``. + + ``nfreqcoag = 1`` (the box calls with the model step, so the + every-3-hours skip logic reduces to "always run"); the ``dqdt`` + diagnostics are not carried (``q`` is updated in place in the + Fortran and returned here). + + Returns the updated ``q``. + """ + from mam4_jax.physics.coag import getcoags_wrapper_f + + tb = _cam_tables(topology) + topo = tb.topology + mait, macc, mpca = tb.mode_aitken, tb.mode_accum, tb.mode_pcarbon + xferfrac_max = 1.0 - 10.0 * float(jnp.finfo(jnp.float64).eps) + + aircon = pmid / (_RGAS_UNIV * t) # kmol-air/m3 + + def numbconc(m): + return jnp.maximum(0.0, q[..., tb.num_ptr[m]] * aircon) + + n_acc, n_ait, n_pca = numbconc(macc), numbconc(mait), numbconc(mpca) + + # Coefficients per pair. (frm, too) play getcoags' (aitken, accum) + # roles; only ij0/ij3/ii0/jj0 are consumed (as in the Fortran). + def betas(mf, mt): + return getcoags_wrapper_f( + t, pmid, + dgncur_awet[..., mf], dgncur_awet[..., mt], + topo.sigmag_amode[mf], topo.sigmag_amode[mt], + float(tb.alnsg[mf]), float(tb.alnsg[mt]), + wetdens_a[..., mf], wetdens_a[..., mt]) + + ij0_aa, _i2a, _j2a, ij3_aa, ii0_aa, _ii2a, jj0_aa, _jj2a = betas(mait, macc) + ij0_pa, _i2b, _j2b, ij3_pa, ii0_pa, _ii2b, jj0_pa, _jj2b = betas(mpca, macc) + ij0_ap, _i2c, _j2c, ij3_ap, ii0_ap, _ii2c, jj0_ap, _jj2c = betas(mait, mpca) + + # --- numbers (:443-500), sequential ------------------------------------ + new_acc = n_acc / (1.0 + deltat * jj0_aa * n_acc) + avg_acc = 0.5 * (new_acc + n_acc) + q = q.at[..., tb.num_ptr[macc]].set(new_acc / aircon) + + new_pca = _coag_number_new( + n_pca, deltat * ij0_pa * avg_acc, deltat * ii0_pa) + avg_pca = 0.5 * (new_pca + n_pca) + q = q.at[..., tb.num_ptr[mpca]].set(new_pca / aircon) + + new_ait = _coag_number_new( + n_ait, deltat * (ij0_aa * avg_acc + ij0_ap * avg_pca), + deltat * ii0_aa) + q = q.at[..., tb.num_ptr[mait]].set(new_ait / aircon) + + # --- aitken mass: combined ait->acc + ait->pca(->acc) (:504-527) ------- + dumloss = ij3_aa * avg_acc + ij3_ap * avg_pca + tmpa_frac = ij3_ap * avg_pca / jnp.maximum(dumloss, 1.0e-37) + xferfracvol = -jnp.expm1(-dumloss * deltat) + xferfracvol = jnp.clip(xferfracvol, 0.0, xferfrac_max) + vol_shell = jnp.zeros_like(dumloss) + for (lf, lt), m2v_age in zip(tb.coag_ait_pairs, tb.fac_m2v_aitage): + xferamt = q[..., lf] * xferfracvol + q = q.at[..., lf].add(-xferamt) + if lt >= 0: + q = q.at[..., lt].add(xferamt) + vol_shell = vol_shell + xferamt * tmpa_frac * m2v_age + + # --- aging fraction (:531-546), same criterion as gasaerexch ----------- + vol_core = jnp.zeros_like(vol_shell) + for s, lw in enumerate(tb.lmass[mpca]): + vol_core = vol_core + q[..., lw] * tb.fac_m2v_pcarbon[s] + tmp1 = vol_shell * dgncur_a[..., mpca] * tb.fac_volsfc_pcarbon + tmp2 = jnp.maximum(6.0 * _DR_SO4_MONOLAYERS_PCAGE * vol_core, 0.0) + saturated = tmp1 >= tmp2 + safe_tmp2 = jnp.where(saturated, 1.0, tmp2) + xferfrac_pcage = jnp.where( + saturated, xferfrac_max, + jnp.minimum(tmp1 / safe_tmp2, xferfrac_max)) + + # --- pcarbon mass + number: direct coag + aging (:550-580) ------------- + dumloss_p = ij3_pa * avg_acc + xferfracvol = -jnp.expm1(-dumloss_p * deltat) + xferfrac_pcage + xferfracvol = jnp.clip(xferfracvol, 0.0, xferfrac_max) + for lf, lt in tb.coag_pca_pairs: + xferamt = q[..., lf] * xferfracvol + q = q.at[..., lf].add(-xferamt) + if lt >= 0: + q = q.at[..., lt].add(xferamt) + xferamt = q[..., tb.num_ptr[mpca]] * xferfrac_pcage + q = q.at[..., tb.num_ptr[mpca]].add(-xferamt) + q = q.at[..., tb.num_ptr[macc]].add(xferamt) + return q + + +# --------------------------------------------------------------------------- +# the sequence — mam_microphysics_cam (mam-box-fortran +# src/coupling/cam/mam_coupling_cam.F90, itself the box transcription of +# aero_model.F90:1202-1247) +# --------------------------------------------------------------------------- + +def mam_microphysics_cam(q, t, pmid, deltat, qv, zm, pblh, + dgncur_a, dgncur_awet, wetdens_a, + del_h2so4_gasprod, *, topology=None, sulfeq=None, + do_gasaerexch=True, do_newnuc=True, do_coag=True): + """CAM's microphysics sequence, one call over ``deltat``. + + ``gasaerexch`` (rename inside) → ``newnuc`` → ``coag``, sequential on + grid-cell means, with the ``del_h2so4_aeruptk`` bookkeeping exactly as + CAM's ``aero_model_gasaerexch`` does it (aero_model.F90:1191-1214, + transcribed in the sibling repo's ``mam_coupling_cam.F90``): the + H2SO4 consumed by condensation is measured as the positive-down + difference across the gasaerexch call and handed to nucleation so the + vapour already condensed is not double-counted. + + Sub-stepping (plan 025 A6) deliberately does NOT live here: this + function is the exact one-call port, and the driver's substep loop + wraps the WHOLE per-step physics (production stub included) so that + ``n_substeps = n`` is semantically identical to running the box at + ``deltat/n`` — the quantity the Fortran dt-convergence study varied. + + ``del_h2so4_gasprod`` is the H2SO4 vmr increment produced by gas + chemistry over THIS call's ``deltat`` (the driver's SO2 stub); it is + input to nucleation only. ``sulfeq`` selects the stratospheric + reversible condensation exactly as in + :func:`modal_aero_gasaerexch_cam`. + + Returns the updated ``q``. + """ + tb = _cam_tables(topology) + + g0 = q[..., tb.l_h2so4] + if do_gasaerexch: + q = modal_aero_gasaerexch_cam( + q, t, pmid, deltat, dgncur_a, dgncur_awet, + topology=topology, sulfeq=sulfeq) + del_h2so4_aeruptk = q[..., tb.l_h2so4] - g0 + + if do_newnuc: + q = modal_aero_newnuc_cam( + q, t, pmid, deltat, qv, zm, pblh, + del_h2so4_gasprod, del_h2so4_aeruptk, topology=topology) + + if do_coag: + q = modal_aero_coag_cam( + q, t, pmid, deltat, dgncur_a, dgncur_awet, wetdens_a, + topology=topology) + return q + + +# --------------------------------------------------------------------------- +# the driver — cam_run_step / cam_run_timesteps (plan 025 G4b) +# (mirrors mam-box-fortran src/driver/mam_box_driver_cam.F90:mam_box_run_cam) +# --------------------------------------------------------------------------- + +def _cam_calcsize_tables(tb: _CamTables): + """CalcsizeTables for a CAM topology, gas-window indexed. + + The csizxf species lists come from RENAME's tables in CAM + (modal_aero_calcsize.F90:42, validated at init :190-211): number + first, then each aitken species name-matched to accum — exactly + ``tb.rename_pairs``. ``noxf_acc2ait`` marks accum slots whose species + prefix has no aitken counterpart (pom, bc). Cloud-borne pointers + equal interstitial ones in both CAM topologies. + """ + from mam4_jax.physics.calcsize import CalcsizeTables + + topo = tb.topology + nm = topo.nmodes + smax = len(topo.lmassptr_amode[0]) + lmass = np.full((nm, smax), -1, dtype=int) + dens = np.ones((nm, smax)) + valid = np.zeros((nm, smax), dtype=bool) + for m in range(nm): + for s_ in range(topo.nspec_amode[m]): + lmass[m, s_] = topo.lmassptr_amode[m][s_] - tb.loffset + dens[m, s_] = topo.specdens_amode[topo.lspectype_amode[m][s_]] + valid[m, s_] = True + + frm = [p[0] for p in tb.rename_pairs] + too = [p[1] for p in tb.rename_pairs] + + mait, macc = tb.mode_aitken, tb.mode_accum + ait_prefixes = { + tb.cnst_names[topo.lmassptr_amode[mait][s_] + - tb.loffset].rsplit("_", 1)[0] + for s_ in range(topo.nspec_amode[mait])} + noxf = np.zeros(smax, dtype=bool) + for s_ in range(topo.nspec_amode[macc]): + pre = tb.cnst_names[topo.lmassptr_amode[macc][s_] + - tb.loffset].rsplit("_", 1)[0] + noxf[s_] = pre not in ait_prefixes + + v2n = topo.voltonumb_amode + return CalcsizeTables( + nait=mait, nacc=macc, nspec_amode=topo.nspec_amode, + lmassptr=lmass, lmassptrcw=lmass, + numptr=tb.num_ptr, numptrcw=tb.num_ptr, + slot_valid=valid, per_slot_density=dens, + voltonumb=v2n, voltonumblo=topo.voltonumblo_amode, + voltonumbhi=topo.voltonumbhi_amode, + dgnum=topo.dgnum_amode, dgnumlo=topo.dgnumlo_amode, + dgnumhi=topo.dgnumhi_amode, dumfac=topo.dumfac_amode, + csizxf_frma=frm, csizxf_tooa=too, + csizxf_frmc=frm, csizxf_tooc=too, + noxf_acc2ait=noxf, + v2nzz=float(np.sqrt(v2n[mait] * v2n[macc])), + ) + + +def _cam_wateruptake_tables(tb: _CamTables): + """WateruptakeTables for a CAM topology, gas-window indexed.""" + from mam4_jax.physics.wateruptake import WateruptakeTables + + topo = tb.topology + nm = topo.nmodes + smax = len(topo.lmassptr_amode[0]) + lmass = np.full((nm, smax), -1, dtype=int) + dens = np.ones((nm, smax)) + hyg = np.zeros((nm, smax)) + valid = np.zeros((nm, smax), dtype=bool) + for m in range(nm): + for s_ in range(topo.nspec_amode[m]): + t_ = topo.lspectype_amode[m][s_] + lmass[m, s_] = topo.lmassptr_amode[m][s_] - tb.loffset + dens[m, s_] = topo.specdens_amode[t_] + hyg[m, s_] = topo.spechygro_amode[t_] + valid[m, s_] = True + return WateruptakeTables( + lmassptr=lmass, slot_valid=valid, per_slot_density=dens, + per_slot_hygro=hyg, sigmag=topo.sigmag_amode, + rhcrystal=topo.rhcrystal_amode, rhdeliques=topo.rhdeliques_amode, + ) + + +def cam_run_step(state, *, topology=None, strat=False, n_substeps=16, + do_calcsize=True, do_wateruptake=True, + do_gasaerexch=True, do_newnuc=True, do_coag=True, + so2_to_h2so4_rate=1.0e-5, + bug_compat_stale_dumfac=False, + first_step=False, + reseed_dgnwet_each_step=True): + """One CAM box-model step (mam_box_run_cam's loop body). + + Per SUBSTEP of ``deltat / n_substeps`` — sub-stepping wraps the WHOLE + physics, so ``n_substeps = n`` is semantically identical to running + the box at ``deltat/n``, the exact quantity the Fortran + dt-convergence study varied. + + **``n_substeps`` defaults to 16 (ADR-021)** — a deliberate deviation + from the defaults-reproduce-the-reference convention, owner-decided + (plan 025 A6): CAM's un-substepped sequential splitting does not + converge while nucleation is active, and n = 1 (CAM's own behaviour, + and the reference box's) is 26-78%% from the converged answer at + dt = 30 s on the default scenario. The error is first-order (halves + per doubling); 16 lands at ~1.4-4.4%% for 16x cost. **Pass + ``n_substeps=1`` to reproduce CAM / the Fortran reference exactly** + — every parity test does. The full measured table is in ADR-021 and + plan 025 §7. + + The per-substep sequence: + + 1. SO2 → H2SO4 first-order conversion (the gas-chemistry stub, + sulfur-mole-conserving by MW ratio; default rate 1e-5 /s = + ``nl_so2_to_h2so4_rate``), producing ``del_h2so4_gasprod`` as a + vmr increment for nucleation; + 2. calcsize (mmr, aitacc transfer on, the fixed per-mode ``dumfac`` + by default — ``bug_compat_stale_dumfac=True`` reproduces upstream + CAM including the bug, matching the non-fixdumfac reference + builds); + 3. ``sulfeq`` when ``strat``: per-mode equilibrium H2SO4 from the + Tabazadeh cluster at the LAGGED wet diameter — the incoming + ``dgncur_awet``, i.e. the previous substep's, exactly as CAM's + pbuf carries it (plan 024 §6's explicit carried state); + 4. wateruptake (mmr; ``qv`` passed explicitly; updates + ``dgncur_awet``/``qaerwat``/``wetdens``); + 5. mmr → vmr over the gas window (``q·mwdry/adv_mass``, number + tracers included with their mechanism ``adv_mass``, exactly as + the box does), the microphysics chain, vmr → mmr back. + + STATE (a dict; all tracers MASS mixing ratio over the gas window): + ``q`` (..., gas_pcnst); ``qv``, ``t``, ``pmid``, ``zm``, ``pblh`` + (...,); ``dgncur_a``, ``dgncur_awet``, ``wetdens`` (..., nmodes); + ``deltat`` scalar. ``qqcw`` is identically zero in scope and not + carried. Returns the updated state dict (same keys, plus + ``qaerwat`` once wateruptake has run). + """ + from mam4_jax.physics.calcsize import calcsize + from mam4_jax.physics.strat_sulfate import calc_h2so4_equilib_mixrat + from mam4_jax.physics.wateruptake import wateruptake + + tb = _cam_tables(topology) + cs_tables = _cam_calcsize_tables(tb) + wu_tables = _cam_wateruptake_tables(tb) + adv = jnp.asarray(tb.adv_mass) + mwdry = tb.mwdry + dt_s = state["deltat"] / n_substeps + + q = jnp.asarray(state["q"], dtype=jnp.float64) + dgncur_a = jnp.asarray(state["dgncur_a"], dtype=jnp.float64) + dgncur_awet = jnp.asarray(state["dgncur_awet"], dtype=jnp.float64) + wetdens = jnp.asarray(state["wetdens"], dtype=jnp.float64) + qaerwat = state.get("qaerwat") + qv, t, pmid = state["qv"], state["t"], state["pmid"] + + so4_slot = np.full(tb.topology.nmodes, -1, dtype=int) + so4_type = tb.topology.specname_amode.index("so4") + for m in range(tb.topology.nmodes): + for s_ in range(tb.topology.nspec_amode[m]): + if tb.topology.lspectype_amode[m][s_] == so4_type: + so4_slot[m] = s_ + dens_so4 = tb.topology.specdens_amode[so4_type] + + for isub in range(n_substeps): + # 1. SO2 -> H2SO4 stub (mam_box_driver_cam.F90:363-373). + if tb.l_so2 >= 0: + prod = q[..., tb.l_so2] * (-jnp.expm1(-so2_to_h2so4_rate * dt_s)) + q = q.at[..., tb.l_so2].add(-prod) + q = q.at[..., tb.l_h2so4].add( + prod * (tb.adv_mass[tb.l_h2so4] / tb.adv_mass[tb.l_so2])) + del_h2so4_gasprod = prod * (mwdry / tb.adv_mass[tb.l_so2]) + else: + del_h2so4_gasprod = jnp.zeros_like(q[..., 0]) + + # 2. calcsize (mmr). + if do_calcsize: + cs = calcsize( + {"q": q, "qqcw": jnp.zeros_like(q), "deltat": dt_s}, + tables=cs_tables, + bug_compat_stale_dumfac=bug_compat_stale_dumfac) + q, dgncur_a = cs["q"], cs["dgncur_a"] + + # CAM's wateruptake_dr seeds the lagged wet diameter from the + # CURRENT dry one under is_first_step() + # (modal_aero_wateruptake.F90:329-331) — BEFORE the sulfeq loop + # reads it. In production CAM that fires once (step 0), making + # sulfeq a genuinely LAGGED-wet-diameter quantity (plan 024 §6's + # carried state). In the box REFERENCE, the time-manager shim's + # is_first_step() is TRUE EVERY STEP (vendor + # time_manager.F90:13-22, never advanced by the driver), so the + # reference recomputes sulfeq from the fresh post-calcsize DRY + # diameters each step and the lag never survives. + # ``reseed_dgnwet_each_step=True`` (default) reproduces the + # reference; False gives the production-CAM lagged behaviour + # (seed on the first step only). Without any seed, step 1's + # sulfeq would see dgncur_awet = 0 and the Kelvin clamp + # evaporates every so4 mode (measured: so4_a1 off by 1e4x). + if do_wateruptake and (reseed_dgnwet_each_step + or (first_step and isub == 0)): + dgncur_awet = dgncur_a + + # 3. sulfeq + Tabazadeh composition at the LAGGED wet diameter + # (before wateruptake updates it) — modal_aero_wateruptake.F90:392-396. + if strat: + dmean = dgncur_awet * jnp.exp(1.5 * jnp.asarray(tb.alnsg) ** 2) + sulfeq, wtpct, sulden = calc_h2so4_equilib_mixrat( + jnp.asarray(t)[..., None], jnp.asarray(pmid)[..., None], + jnp.asarray(qv)[..., None], dmean) + strat_wu = {"so4_slot": so4_slot, "so4specdens": dens_so4, + "wtpct": wtpct, "sulden": sulden} + else: + sulfeq = None + strat_wu = None + + # 4. wateruptake (mmr; qv explicit; the strat branch replaces + # Köhler with the wt%-composition solution volume — the box sets + # its tropopause above the single level, so under strat that + # branch is live everywhere). + if do_wateruptake: + wu = wateruptake( + {"q": q, "dgncur_a": dgncur_a, "t": t, "pmid": pmid, + "cldn": jnp.zeros_like(jnp.asarray(t))}, + tables=wu_tables, qv=qv, strat=strat_wu) + dgncur_awet = wu["dgncur_awet"] + qaerwat = wu["qaerwat"] + wetdens = wu["wetdens"] + + # 5. the microphysics chain, on vmr. + q_vmr = q * (mwdry / adv) + q_vmr = mam_microphysics_cam( + q_vmr, t, pmid, dt_s, qv, state["zm"], state["pblh"], + dgncur_a, dgncur_awet, wetdens, del_h2so4_gasprod, + topology=topology, sulfeq=sulfeq, + do_gasaerexch=do_gasaerexch, do_newnuc=do_newnuc, + do_coag=do_coag) + q = q_vmr * (adv / mwdry) + + out = {**state, "q": q, "dgncur_a": dgncur_a, + "dgncur_awet": dgncur_awet, "wetdens": wetdens} + if qaerwat is not None: + out["qaerwat"] = qaerwat + return out + + +def cam_run_timesteps(state, n_steps, **kwargs): + """Run ``n_steps`` CAM box steps; return the final state plus a + trajectory dict of stacked per-step snapshots of ``q``, + ``dgncur_a``, ``dgncur_awet``, ``wetdens`` (post-step values, + matching the Fortran box's per-step output rows). Plain Python loop + — phase A; jit/scan is the phase-B optimization pass.""" + import jax + + traj = {k: [] for k in ("q", "dgncur_a", "dgncur_awet", "wetdens")} + for istep in range(n_steps): + state = cam_run_step(state, first_step=(istep == 0), **kwargs) + for k in traj: + traj[k].append(state[k]) + stacked = {k: jax.numpy.stack(v) for k, v in traj.items()} + return state, stacked diff --git a/mam4_jax/driver.py b/mam4_jax/driver.py index b45ef2e..a150284 100644 --- a/mam4_jax/driver.py +++ b/mam4_jax/driver.py @@ -62,7 +62,7 @@ import jax import jax.numpy as jnp -from .coupling.amicphys import amicphys +from .coupling.amicphys import _check_clear_sky, amicphys from .physics.calcsize import calcsize from .physics.wateruptake import wateruptake @@ -80,8 +80,8 @@ def cloud_chem_simple_sub(state: dict[str, Any]) -> dict[str, Any]: @functools.partial(jax.jit, static_argnames=("mdo_pcarbonaging",)) -def run_step(state: dict[str, Any], params=None, *, - mdo_pcarbonaging: int = 1) -> dict[str, Any]: +def _run_step_jit(state: dict[str, Any], params=None, *, + mdo_pcarbonaging: int = 1) -> dict[str, Any]: """One operator-splitting timestep. Sequence mirrors ``driver.F90:1080-1367`` (``main_time_loop``): @@ -127,8 +127,8 @@ def run_step(state: dict[str, Any], params=None, *, @functools.partial(jax.jit, static_argnames=("n_steps", "mdo_pcarbonaging")) -def run_timesteps(state: dict[str, Any], n_steps: int, params=None, *, - mdo_pcarbonaging: int = 1) -> dict[str, Any]: +def _run_timesteps_jit(state: dict[str, Any], n_steps: int, params=None, *, + mdo_pcarbonaging: int = 1) -> dict[str, Any]: """Run ``n_steps`` operator-splitting timesteps and return a stacked trajectory. @@ -170,9 +170,9 @@ def run_timesteps(state: dict[str, Any], n_steps: int, params=None, *, paid ~1 s of Python overhead, which dominated benchmarks that invoke ``run_timesteps`` many times (e.g. 1000-sim wall-time studies). Inside the JIT'd ``run_timesteps``, scan calls - ``run_step`` with the 16-key augmented carry; direct callers of - ``run_step`` (e.g. ``tests/test_driver.py``) pass a 13-key state - and get their own ``run_step`` cache entry. Both compiles are + ``_run_step_jit`` with the 16-key augmented carry; direct callers + of ``run_step`` (e.g. ``tests/test_driver.py``) pass a 13-key state + and get their own ``_run_step_jit`` cache entry. Both compiles are ~1-2 s each on this hardware. """ if n_steps < 1: @@ -200,8 +200,8 @@ def run_timesteps(state: dict[str, Any], n_steps: int, params=None, *, def _scan_body(carry_state: dict[str, Any], _) -> tuple[ dict[str, Any], dict[str, Any] ]: - new_state = run_step(carry_state, params, - mdo_pcarbonaging=mdo_pcarbonaging) + new_state = _run_step_jit(carry_state, params, + mdo_pcarbonaging=mdo_pcarbonaging) output = {k: new_state[k] for k in _TRAJ_KEYS} return new_state, output @@ -209,3 +209,35 @@ def _scan_body(carry_state: dict[str, Any], _) -> tuple[ _scan_body, augmented, xs=None, length=n_steps, ) return trajectory + + +# --------------------------------------------------------------------------- +# Public entries. Thin, UNJITTED wrappers whose only job is to validate before +# tracing begins. +# +# The jitted implementations above cannot do this themselves: inside a trace +# `cldn` is a tracer with no readable magnitude, so a check there can never fire +# on the normal path. Only the clear-sky sub-area of amicphys is ported, and a +# non-zero cloud fraction would otherwise get clear-sky physics applied to the +# whole cell -- a plausible-looking wrong answer. +# +# The wrappers add one Python-level call per step and no tracing overhead; the +# jit cache still lives on the inner functions. +# --------------------------------------------------------------------------- + +def run_step(state: dict[str, Any], params=None, *, + mdo_pcarbonaging: int = 1) -> dict[str, Any]: + """One operator-splitting timestep. See :func:`_run_step_jit`.""" + _check_clear_sky(state.get("cldn")) + return _run_step_jit(state, params, mdo_pcarbonaging=mdo_pcarbonaging) + + +def run_timesteps(state: dict[str, Any], n_steps: int, params=None, *, + mdo_pcarbonaging: int = 1) -> dict[str, Any]: + """Run ``n_steps`` timesteps, returning a stacked trajectory. + + See :func:`_run_timesteps_jit`. + """ + _check_clear_sky(state.get("cldn")) + return _run_timesteps_jit(state, n_steps, params, + mdo_pcarbonaging=mdo_pcarbonaging) diff --git a/mam4_jax/physics/calcsize.py b/mam4_jax/physics/calcsize.py index f9517f9..6d16bea 100644 --- a/mam4_jax/physics/calcsize.py +++ b/mam4_jax/physics/calcsize.py @@ -84,6 +84,62 @@ # line 627 — tadj = 86400 (1 day adjustment time scale) # line 748 — frelaxadj = 27 (= 3^3; relaxed bounds = strict ÷ frelaxadj # on the upper side and × frelaxadj on the lower) + + +class CalcsizeTables: + """Every mode/species table calcsize reads, as one bundle. + + The default instance (`_E3SM_TABLES`, built from the module constants + imported above) keeps the E3SM path bit-identical; the CAM driver + builds instances from a `Topology` + `cam_params` with indices in its + own state coordinate (the gas window). Plain numpy / Python scalars — + static under jit. + """ + + def __init__(self, *, nait, nacc, nspec_amode, + lmassptr, lmassptrcw, numptr, numptrcw, + slot_valid, per_slot_density, + voltonumb, voltonumblo, voltonumbhi, + dgnum, dgnumlo, dgnumhi, dumfac, + csizxf_frma, csizxf_tooa, csizxf_frmc, csizxf_tooc, + noxf_acc2ait, v2nzz): + self.nait, self.nacc = int(nait), int(nacc) + self.nspec_amode = np.asarray(nspec_amode) + self.lmassptr = np.asarray(lmassptr) + self.lmassptrcw = np.asarray(lmassptrcw) + self.numptr = np.asarray(numptr) + self.numptrcw = np.asarray(numptrcw) + self.slot_valid = np.asarray(slot_valid) + self.per_slot_density = np.asarray(per_slot_density) + self.voltonumb = np.asarray(voltonumb) + self.voltonumblo = np.asarray(voltonumblo) + self.voltonumbhi = np.asarray(voltonumbhi) + self.dgnum = np.asarray(dgnum) + self.dgnumlo = np.asarray(dgnumlo) + self.dgnumhi = np.asarray(dgnumhi) + self.dumfac = np.asarray(dumfac) + self.csizxf_frma = np.asarray(csizxf_frma) + self.csizxf_tooa = np.asarray(csizxf_tooa) + self.csizxf_frmc = np.asarray(csizxf_frmc) + self.csizxf_tooc = np.asarray(csizxf_tooc) + self.noxf_acc2ait = np.asarray(noxf_acc2ait) + self.v2nzz = float(v2nzz) + + +_E3SM_TABLES = CalcsizeTables( + nait=AITKEN_MODE_IDX, nacc=ACCUM_MODE_IDX, nspec_amode=NSPEC_AMODE, + lmassptr=INDEX_TABLES.lmassptr_amode, + lmassptrcw=INDEX_TABLES.lmassptrcw_amode, + numptr=INDEX_TABLES.numptr_amode, numptrcw=INDEX_TABLES.numptrcw_amode, + slot_valid=SLOT_VALID, per_slot_density=PER_SLOT_DENSITY, + voltonumb=VOLTONUMB_AMODE, voltonumblo=VOLTONUMBLO_AMODE, + voltonumbhi=VOLTONUMBHI_AMODE, + dgnum=DGNUM_AMODE, dgnumlo=DGNUMLO_AMODE, dgnumhi=DGNUMHI_AMODE, + dumfac=DUMFAC_AMODE, + csizxf_frma=LSPECFRMA_CSIZXF, csizxf_tooa=LSPECTOOA_CSIZXF, + csizxf_frmc=LSPECFRMC_CSIZXF, csizxf_tooc=LSPECTOOC_CSIZXF, + noxf_acc2ait=NOXF_ACC2AIT, v2nzz=V2NZZ_AIT_ACC, +) _THIRD = 1.0 / 3.0 _TADJ_S = 86400.0 _FRELAXADJ = 27.0 @@ -269,6 +325,7 @@ def _apply_aitacc_transfer( drv_a: jnp.ndarray, drv_c: jnp.ndarray, q: jnp.ndarray, qqcw: jnp.ndarray, deltat: jnp.ndarray, tadj_inv: jnp.ndarray, + tb: CalcsizeTables, ): """Apply Fortran's Aitken ↔ accumulation transfer (lines 944–1294). @@ -284,12 +341,12 @@ def _apply_aitacc_transfer( the caller needs them; they were previously discarded, which is why that block had no counterpart here. """ - nait = AITKEN_MODE_IDX - nacc = ACCUM_MODE_IDX - v2nzz = float(V2NZZ_AIT_ACC) - v2n_acc = float(VOLTONUMB_AMODE[nacc]) - v2n_ait = float(VOLTONUMB_AMODE[nait]) - v2nlo_acc = float(VOLTONUMBLO_AMODE[nacc]) + nait = tb.nait + nacc = tb.nacc + v2nzz = float(tb.v2nzz) + v2n_acc = float(tb.voltonumb[nacc]) + v2n_ait = float(tb.voltonumb[nait]) + v2nlo_acc = float(tb.voltonumblo[nacc]) # --- aitken → accum rates (Fortran lines 1010-1045) ------------------- num_a_ait = num_a[..., nait] @@ -318,12 +375,12 @@ def _apply_aitacc_transfer( # No-transfer species mass: accum slots whose species type isn't in Aitken. drv_a_noxf = jnp.zeros_like(drv_a_acc) drv_c_noxf = jnp.zeros_like(drv_c_acc) - for s in range(int(NSPEC_AMODE[nacc])): - if not NOXF_ACC2AIT[s]: + for s in range(int(tb.nspec_amode[nacc])): + if not tb.noxf_acc2ait[s]: continue - idx_a = int(LMASSPTR_AMODE[nacc][s]) - idx_c = int(LMASSPTRCW_AMODE[nacc][s]) - density = float(PER_SLOT_DENSITY[nacc, s]) + idx_a = int(tb.lmassptr[nacc][s]) + idx_c = int(tb.lmassptrcw[nacc][s]) + density = float(tb.per_slot_density[nacc, s]) drv_a_noxf = drv_a_noxf + jnp.maximum(q[..., idx_a], 0.0) / density drv_c_noxf = drv_c_noxf + jnp.maximum(qqcw[..., idx_c], 0.0) / density drv_t_noxf = drv_a_noxf + drv_c_noxf @@ -383,11 +440,11 @@ def _apply_aitacc_transfer( # at lsfrm (aitken) and lstoo (accum) with opposite signs. new_q = q new_qqcw = qqcw - for iq in range(int(LSPECFRMA_CSIZXF.shape[0])): - lsfrm = int(LSPECFRMA_CSIZXF[iq]) # aitken pcnst idx (interstitial) - lstoo = int(LSPECTOOA_CSIZXF[iq]) # accum pcnst idx - lsfrm_c = int(LSPECFRMC_CSIZXF[iq]) - lstoo_c = int(LSPECTOOC_CSIZXF[iq]) + for iq in range(int(tb.csizxf_frma.shape[0])): + lsfrm = int(tb.csizxf_frma[iq]) # aitken state idx (interstitial) + lstoo = int(tb.csizxf_tooa[iq]) # accum state idx + lsfrm_c = int(tb.csizxf_frmc[iq]) + lstoo_c = int(tb.csizxf_tooc[iq]) if iq == 0: # Number tracer pair — total delta is computed by net of the @@ -444,7 +501,8 @@ def _compute_dgn_v2n(num: jnp.ndarray, drv: jnp.ndarray, def calcsize(state: dict[str, Any], params=None, config=None, *, do_aitacc_transfer: bool = True, - bug_compat_stale_dumfac: bool = False) -> dict[str, Any]: + bug_compat_stale_dumfac: bool = False, + tables: CalcsizeTables | None = None) -> dict[str, Any]: """Apply size redistribution. ADR-009 entry point. Args: @@ -457,8 +515,13 @@ def calcsize(state: dict[str, Any], params=None, config=None, stops after the per-mode adjustment — matches the Fortran ``do_aitacc_transfer_in=.false.`` reference at ``tests/reference/per_process_no_aitacc/``. + tables: mode/species tables, ``None`` (default) = the E3SM + MAM4-MOM constants — bit-identical to the pre-parameter + behaviour. The CAM driver passes topology-derived tables + with indices in ITS state coordinate (plan 025 G4b). """ del params, config + tb = _E3SM_TABLES if tables is None else tables q = jnp.asarray(state["q"], dtype=jnp.float64) qqcw = jnp.asarray(state["qqcw"], dtype=jnp.float64) @@ -467,16 +530,16 @@ def calcsize(state: dict[str, Any], params=None, config=None, # but calcsize derives its own new value below. # Index tables and per-(mode, slot) species properties. - lmass_idx = jnp.asarray(INDEX_TABLES.lmassptr_amode, dtype=jnp.int32) - lmass_idx_cw = jnp.asarray(INDEX_TABLES.lmassptrcw_amode, dtype=jnp.int32) - numptr = jnp.asarray(INDEX_TABLES.numptr_amode, dtype=jnp.int32) - numptr_cw = jnp.asarray(INDEX_TABLES.numptrcw_amode, dtype=jnp.int32) - slot_mask = jnp.asarray(SLOT_VALID, dtype=jnp.float64) - per_slot_density = jnp.asarray(PER_SLOT_DENSITY) + lmass_idx = jnp.asarray(tb.lmassptr, dtype=jnp.int32) + lmass_idx_cw = jnp.asarray(tb.lmassptrcw, dtype=jnp.int32) + numptr = jnp.asarray(tb.numptr, dtype=jnp.int32) + numptr_cw = jnp.asarray(tb.numptrcw, dtype=jnp.int32) + slot_mask = jnp.asarray(tb.slot_valid, dtype=jnp.float64) + per_slot_density = jnp.asarray(tb.per_slot_density) # Per-mode bound constants (broadcast as (m,)). - v2nxx = jnp.asarray(VOLTONUMBHI_AMODE) - v2nyy = jnp.asarray(VOLTONUMBLO_AMODE) + v2nxx = jnp.asarray(tb.voltonumbhi) + v2nyy = jnp.asarray(tb.voltonumblo) if do_aitacc_transfer: # The Fortran deliberately disables the size bounds on the two modes # taking part in the aitken<->accum transfer, so the transfer block -- @@ -491,18 +554,18 @@ def calcsize(state: dict[str, Any], params=None, config=None, # Omitting it clamped number where the reference does not. # do_aitacc_transfer is a Python bool, so this branch is static under # jit and costs nothing at trace time. - v2nxx = v2nxx.at[AITKEN_MODE_IDX].divide(1.0e6) - v2nyy = v2nyy.at[ACCUM_MODE_IDX].multiply(1.0e6) + v2nxx = v2nxx.at[tb.nait].divide(1.0e6) + v2nyy = v2nyy.at[tb.nacc].multiply(1.0e6) # Both trees recompute the relaxed bounds AFTER that adjustment (the "NEW" # comments at CAM :559-560 / E3SM :759-760), so the relaxed pair inherits # the turned-off bounds. With do_aitacc_transfer False these derive from # the untouched values, matching the Fortran's pre-branch assignment. v2nxxrl = v2nxx / _FRELAXADJ v2nyyrl = v2nyy * _FRELAXADJ - dgnxx = jnp.asarray(DGNUMHI_AMODE) - dgnyy = jnp.asarray(DGNUMLO_AMODE) - dumfac = jnp.asarray(DUMFAC_AMODE) - voltonumb_amode = jnp.asarray(VOLTONUMB_AMODE) + dgnxx = jnp.asarray(tb.dgnumhi) + dgnyy = jnp.asarray(tb.dgnumlo) + dumfac = jnp.asarray(tb.dumfac) + voltonumb_amode = jnp.asarray(tb.voltonumb) # Adjustment time scale (Fortran lines 626–631). tadj = jnp.maximum(_TADJ_S, deltat) @@ -565,7 +628,7 @@ def calcsize(state: dict[str, Any], params=None, config=None, q_post_transfer, qqcw_post_transfer, ixfer_ait2acc, ixfer_acc2ait) = _apply_aitacc_transfer( num_a_final, num_c_final, drv_a, drv_c, q, qqcw, - deltat, tadj_inv, + deltat, tadj_inv, tb, ) xfer_fired = ixfer_ait2acc | ixfer_acc2ait else: @@ -577,7 +640,7 @@ def calcsize(state: dict[str, Any], params=None, config=None, # When drv <= 0 the Fortran loop keeps the per-mode defaults # (dgnum_amode, voltonumb_amode) that were set at the top of the loop. # We mirror that with a final jnp.where fallback. - dgnum_amode = jnp.asarray(DGNUM_AMODE) + dgnum_amode = jnp.asarray(tb.dgnum) dgncur_a_new, v2ncur_a_new = _compute_dgn_v2n( num_a_final, drv_a, v2nxx, v2nyy, dgnxx, dgnyy, dumfac, @@ -619,21 +682,21 @@ def calcsize(state: dict[str, Any], params=None, config=None, # The Fortran comment "! currently inactive" at :933 describes a regime in # which no transfer fires, not a disabled code path. if do_aitacc_transfer: - v2nhi_raw = jnp.asarray(VOLTONUMBHI_AMODE) - v2nlo_raw = jnp.asarray(VOLTONUMBLO_AMODE) - dgnhi_raw = jnp.asarray(DGNUMHI_AMODE) - dgnlo_raw = jnp.asarray(DGNUMLO_AMODE) + v2nhi_raw = jnp.asarray(tb.voltonumbhi) + v2nlo_raw = jnp.asarray(tb.voltonumblo) + dgnhi_raw = jnp.asarray(tb.dgnumhi) + dgnlo_raw = jnp.asarray(tb.dgnumlo) if bug_compat_stale_dumfac: # The value CAM is left holding: the last mode's. - dumfac_post = jnp.full_like(jnp.asarray(DUMFAC_AMODE), - float(DUMFAC_AMODE[-1])) + dumfac_post = jnp.full_like(jnp.asarray(tb.dumfac), + float(tb.dumfac[-1])) else: - dumfac_post = jnp.asarray(DUMFAC_AMODE) + dumfac_post = jnp.asarray(tb.dumfac) # Only the two transfer lanes are rewritten. - lane = np.zeros(len(NSPEC_AMODE), dtype=bool) - lane[AITKEN_MODE_IDX] = True - lane[ACCUM_MODE_IDX] = True + lane = np.zeros(len(tb.nspec_amode), dtype=bool) + lane[tb.nait] = True + lane[tb.nacc] = True lane = jnp.asarray(lane) sel = jnp.asarray(xfer_fired)[..., None] & lane diff --git a/mam4_jax/physics/cam_saturation.py b/mam4_jax/physics/cam_saturation.py new file mode 100644 index 0000000..dea0186 --- /dev/null +++ b/mam4_jax/physics/cam_saturation.py @@ -0,0 +1,98 @@ +"""CAM's table-interpolated mixed-phase saturation — ``qsat`` / ``estblf``. + +The CESM3 ``wv_saturation`` module serves TWO different saturation answers: + +* ``qsat_water`` — direct Goff-Gratch over liquid water (already ported + privately by :mod:`mam4_jax.physics.strat_sulfate`, whose Tabazadeh + composition calls it); +* the generic ``qsat`` — a LOOKUP TABLE (``estbl``) built at init over + ``tmin = 127.16`` … ``tmax = 375.16`` K at 1 K spacing from + ``svp_trans``: Goff-Gratch over water above ``tmelt``, Goff-Gratch over + ice below ``tmelt - ttrice`` (ttrice = 20 K), and a linear water/ice + blend in between — then linearly interpolated in temperature + (``estblf``, wv_saturation.F90:378-393). + +CAM's ``modal_aero_newnuc_sub`` computes its relative humidity through the +GENERIC ``qsat`` (:246), so the CAM driver must reproduce the table, not +the direct formula: at stratospheric temperatures the two differ by the +full water-vs-ice SVP ratio (~2x at 200 K), and the table's 1 K linear +interpolation is itself a (small) part of the reference answer. + +The table is built once at import with numpy — the same 250 entries the +Fortran builds in ``wv_sat_init``, bit-for-bit (same formulas, same +constants, same order of operations per entry). +""" +from __future__ import annotations + +import jax.numpy as jnp +import numpy as np + +_TMIN = 127.16 +_TMAX = 375.16 +_TMELT = 273.15 # shr_const_tkfrz +_TTRICE = 20.00 # wv_saturation.F90:98 +_H2OTRIP = 273.16 # shr_const_tktrip +_TBOIL = 373.16 # wv_saturation.F90:87 +_EPSILO = 18.016 / 28.966 +_OMEPS = 1.0 - _EPSILO + + +def _svp_water_np(t): + """GoffGratch_svp_water (wv_sat_methods.F90:569-580), numpy scalar.""" + return 10.0 ** ( + -7.90298 * (_TBOIL / t - 1.0) + + 5.02808 * np.log10(_TBOIL / t) + - 1.3816e-7 * (10.0 ** (11.344 * (1.0 - t / _TBOIL)) - 1.0) + + 8.1328e-3 * (10.0 ** (-3.49149 * (_TBOIL / t - 1.0)) - 1.0) + + np.log10(1013.246) + ) * 100.0 + + +def _svp_ice_np(t): + """GoffGratch_svp_ice (wv_sat_methods.F90, 'good down to -100 C').""" + return 10.0 ** ( + -9.09718 * (_H2OTRIP / t - 1.0) + - 3.56654 * np.log10(_H2OTRIP / t) + + 0.876793 * (1.0 - t / _H2OTRIP) + + np.log10(6.1071) + ) * 100.0 + + +def _svp_trans_np(t): + """wv_sat_svp_trans: water above tmelt, ice below tmelt - ttrice, + linear blend between (weight = (tmelt - t)/ttrice).""" + es = _svp_water_np(t) if t >= (_TMELT - _TTRICE) else 0.0 + if t < _TMELT: + esice = _svp_ice_np(t) + weight = 1.0 if (_TMELT - t) > _TTRICE else (_TMELT - t) / _TTRICE + es = weight * esice + (1.0 - weight) * es + return es + + +#: The Fortran table: plenest = ceiling(tmax - tmin) + 2 = 250 entries at +#: ``tmin + (i - 1)`` K (wv_saturation.F90:235-246). +_PLENEST = int(np.ceil(_TMAX - _TMIN)) + 2 +_ESTBL = np.array([_svp_trans_np(_TMIN + float(i)) for i in range(_PLENEST)]) + + +def estblf_cam(t): + """Linear table interpolation of mixed-phase SVP (Pa) — + ``estblf`` (wv_saturation.F90:378-393).""" + t_tmp = jnp.maximum(jnp.minimum(t, _TMAX) - _TMIN, 0.0) + i = jnp.floor(t_tmp).astype(jnp.int32) # Fortran int() + 1, 0-based + weight = t_tmp - jnp.floor(t_tmp) # aint == floor for t_tmp >= 0 + tbl = jnp.asarray(_ESTBL) + return (1.0 - weight) * tbl[i] + weight * tbl[i + 1] + + +def qsat_cam(t, p): + """CAM's generic ``qsat`` (mixed-phase, table): returns ``(es, qs)``. + + ``qs = 1`` when ``p <= es`` (``wv_sat_svp_to_qsat``), and the returned + ``es`` is capped at ``p`` for consistency — both exactly as + ``qsat_line/vect`` do.""" + es = estblf_cam(t) + saturated = (p - es) <= 0.0 + safe_den = jnp.where(saturated, 1.0, p - _OMEPS * es) + qs = jnp.where(saturated, 1.0, _EPSILO * es / safe_den) + return jnp.minimum(es, p), qs diff --git a/mam4_jax/physics/newnuc.py b/mam4_jax/physics/newnuc.py index dcd3911..5e2c30b 100644 --- a/mam4_jax/physics/newnuc.py +++ b/mam4_jax/physics/newnuc.py @@ -244,7 +244,8 @@ def pbl_nuc_wang2008(so4vol, flagaa, def mer07_veh02_nuc_mosaic_1box(dtnuc, temp, rh, press, zm, pblh, qh2so4_cur, qh2so4_avg, h2so4_uptkrate, dplom_sect, dphim_sect, - newnuc_method_flagaa=11): + newnuc_method_flagaa=11, + mw_so4a_host=None): """Port of ``mer07_veh02_nuc_mosaic_1box`` (``modal_aero_newnuc.F90:598-1173``). Dispatcher that wraps the PR-F1 leaf parameterizations @@ -285,6 +286,12 @@ def mer07_veh02_nuc_mosaic_1box(dtnuc, temp, rh, press, zm, pblh, 1 in MAM4-MOM — Aitken-mode lo/hi from ``data.DGNUMLO_AMODE``). newnuc_method_flagaa : int Static (Python int). 11 = first-order PBL (Fortran default). + mw_so4a_host : float, optional + Molecular weight of sulfate aerosol in the HOST code (g/mol) — + the Fortran passes this as an argument for the same reason. + ``None`` (default) resolves to ``data.MW_SO4A_HOST`` (115.0, the + E3SM box value), leaving the E3SM path bit-unchanged; the CAM + driver passes its topology's 115.10734. Returns ------- @@ -306,6 +313,8 @@ def mer07_veh02_nuc_mosaic_1box(dtnuc, temp, rh, press, zm, pblh, Cluster nucleation rate (#/m³/s). """ # Local constants from Fortran scope. + if mw_so4a_host is None: + mw_so4a_host = data.MW_SO4A_HOST rgas_local = _RGAS_J_PER_K_PER_KMOL / 1.0e3 # J/K/mol (vs J/K/kmol) avogad = 6.02214e26 / 1.0e3 # 1/mol (vs 1/kmol) pi = jnp.pi @@ -372,7 +381,7 @@ def mer07_veh02_nuc_mosaic_1box(dtnuc, temp, rh, press, zm, pblh, voldry_clus = (jnp.maximum(cnum_h2so4, 1.0) * _MW_SO4A + cnum_nh3 * _MW_NH4A) / ( 1.0e3 * _DENS_SULFACID * avogad ) - voldry_clus = voldry_clus * (data.MW_SO4A_HOST / _MW_SO4A) + voldry_clus = voldry_clus * (mw_so4a_host / _MW_SO4A) dpdry_clus = (voldry_clus * 6.0 / pi) ** onethird isize_nuc = jnp.ones_like(jnp.asarray(so4vol_in), dtype=jnp.int32) @@ -394,7 +403,7 @@ def mer07_veh02_nuc_mosaic_1box(dtnuc, temp, rh, press, zm, pblh, dens_nh4so4a = jnp.full_like(rateloge, dens_part) mass_part = voldry_part * dens_part molenh4a_per_moleso4a = 0.0 - kgaero_per_moleso4a = 1.0e-3 * _MW_SULFACID * (data.MW_SO4A_HOST / _MW_SO4A) + kgaero_per_moleso4a = 1.0e-3 * _MW_SULFACID * (mw_so4a_host / _MW_SO4A) # Stage 8: wet volume fraction. tmpb_wvf = 1.0 + molenh4a_per_moleso4a * 17.0 / 98.0 diff --git a/mam4_jax/physics/strat_sulfate.py b/mam4_jax/physics/strat_sulfate.py new file mode 100644 index 0000000..39fa6dd --- /dev/null +++ b/mam4_jax/physics/strat_sulfate.py @@ -0,0 +1,401 @@ +"""Stratospheric sulfate equilibrium — JAX port of CAM's ``sulfeq`` cluster. + +CAM-only physics (plan 024 PR H / plan 025 remaining item 1): above the +tropopause, CAM treats H2SO4 condensation as REVERSIBLE, limited by the +equilibrium H2SO4 mixing ratio over each mode's particles (``sulfeq``), +instead of E3SM/amicphys' irreversible uptake. The equilibrium value is +computed per mode inside CAM's water uptake from the Tabazadeh weight-percent +composition, Ayers/Kulmala vapor pressure, and a Kelvin curvature factor. + +Ported line-by-line from the CESM3 snapshot vendored in the sibling repo +``mam-box-fortran`` (pinned in its ``PROVENANCE.md`` to ``cam6_4_187``): + +* :func:`calc_h2so4_wtpct` — ``modal_aero_wateruptake.F90:1087-1171``. + Weight % H2SO4 of sulfate aerosol vs water activity (Tabazadeh et al., + GRL 1997; rated T=185-260 K, activity 0.01-1.0). +* :func:`calc_h2so4_equilib_mixrat` — ``modal_aero_wateruptake.F90:895-1083``. + Equilibrium H2SO4 mixing ratio over particles of mean diameter ``dmean``, + plus the (Kelvin-adjusted) composition and sulfate density. +* :func:`h2so4_reversible_uptake` — ``modal_aero_gasaerexch.F90:523-566``. + The consumer: per-mode so4 tendencies relaxing the gas toward the + mode-weighted equilibrium (over-saturated modes evaporate). +* :func:`_qsat_water_cam` — CAM's ``wv_sat_methods.F90`` Goff-Gratch + + ``wv_sat_svp_to_qsat``. NOT the same as :mod:`mam4_jax.physics.saturation` + (the E3SM box ``qsat_water``): CAM returns ``qs = 1`` whenever ``p <= es``, + the E3SM box clamps only when the denominator has gone negative + (``qs < 0``). The two disagree on ``es in [p, p/(1-epsilo)]`` — reachable + at the ``t = 450 K`` clamp edge — so the CAM cluster carries its own + helper rather than reusing the E3SM one. + +Faithfulness notes (upstream oddities preserved, not fixed): + +* **First surface-tension interpolation uses a mismatched abscissa** + (F90:1005): ``surf_tens = sig1 + dsigma_dwt*(wtpct_flat - stwtp(i))`` + pairs ``sig1`` (the ``i-1`` knot's ordinate) with the ``i`` knot's + abscissa, so ``surf_tens`` is offset by ``-(sig2-sig1)`` relative to a + correct linear interpolation. The second lookup (F90:1032-1036, ``frac`` + form) is correct. Ported as-is; recorded in mam-box-fortran + ``docs/bugs/``. +* The Kelvin factor MULTIPLIES the equilibrium ratio by ``exp(+akelvin/r)`` + (> 1); the upstream comment says "reduce". The arithmetic is what is + ported. +* ``deltat`` does not appear: the equilibrium is diagnostic per call. + +Everything here is a pure element-wise function of scalars/arrays +(broadcasting), float64 under the package default, no ``jit`` (phase A — +callers compose and jit). Reverse-mode safe: every branch is a +``jnp.where`` over operands computed on a clipped-to-branch-domain copy of +the input, so no dead branch produces a NaN/Inf cotangent. + +Validated at float64 machine precision against +``tests/reference/cam_sulfeq/sulfeq.json``, captured from the Fortran by +``mam-box-fortran/tools/capture_sulfeq``; see ``tests/test_strat_sulfate.py``. +""" +from __future__ import annotations + +import jax.numpy as jnp +import numpy as np + +# --------------------------------------------------------------------------- +# Constants (modal_aero_wateruptake.F90:918-926). RGAS here is the CGS ideal +# gas constant in erg/mol/K — a deliberate private copy, same policy as the +# Köhler CGS island (plan 024 §3: do NOT normalise to core.constants). +# --------------------------------------------------------------------------- +_T0_KULM = 340.0 # K, low end of Ayers' range +_T_CRIT_KULM = 905.0 # K, 1.5 x boiling point +_FK0 = -10156.0 / _T0_KULM + 16.259 # log of Kulmala correction factor +_FK2 = 1.0 / _T0_KULM +_FK3 = 0.38 / (_T_CRIT_KULM - _T0_KULM) +_RGAS_CGS = 8.31430e7 # erg/mol/K +_WTMOL_H2SO4 = 98.078479 # g/mol + +# CAM wv_sat: tboil (wv_saturation.F90:87) and epsilo = mwwv/mwdair +# (shr_const_mod.F90:27-28) — numerically identical to core.constants.EPSQS; +# spelled out here so the CAM cluster is self-contained and auditable +# against its own Fortran. +_TBOIL = 373.16 # K +_EPSILO = 18.016 / 28.966 +_OMEPS = 1.0 - _EPSILO + +# --- surface tension vs (wt%, T): sigma = stc0 + stc1*T at each knot ------- +# (modal_aero_wateruptake.F90:932-944) +_STWTP = np.array([ + 0.0, 23.8141, 38.0279, 40.6856, 45.335, 52.9305, + 56.2735, 59.8557, 66.2364, 73.103, 79.432, 85.9195, + 91.7444, 97.6687, 100.0]) +_STC0 = np.array([ + 117.564, 103.303, 101.796, 100.42, 98.4993, 91.8866, + 88.3033, 86.5546, 84.471, 81.2939, 79.3556, 75.608, + 70.0777, 63.7412, 61.4591]) +_STC1 = np.array([ + -0.153641, -0.0982007, -0.0872379, -0.0818509, + -0.0746702, -0.0522399, -0.0407773, -0.0357946, -0.0317062, + -0.025825, -0.0267212, -0.0269204, -0.0276187, -0.0302094, + -0.0303081]) + +# --- density vs (wt%, T): rho = dnc0 + dnc1*T at each knot ------------------ +# (modal_aero_wateruptake.F90:947-969) +_DNWTP = np.array([ + 0.0, 1.0, 5.0, 10.0, 20.0, 25.0, 30.0, 35.0, 40.0, + 41.0, 45.0, 50.0, 53.0, 55.0, 56.0, 60.0, 65.0, 66.0, 70.0, + 72.0, 73.0, 74.0, 75.0, 76.0, 78.0, 79.0, 80.0, 81.0, 82.0, + 83.0, 84.0, 85.0, 86.0, 87.0, 88.0, 89.0, 90.0, 91.0, 92.0, + 93.0, 94.0, 95.0, 96.0, 97.0, 98.0, 100.0]) +_DNC0 = np.array([ + 1.0, 1.13185, 1.17171, 1.22164, 1.3219, 1.37209, + 1.42185, 1.4705, 1.51767, 1.52731, 1.56584, 1.61834, 1.65191, + 1.6752, 1.68708, 1.7356, 1.7997, 1.81271, 1.86696, 1.89491, + 1.9092, 1.92395, 1.93904, 1.95438, 1.98574, 2.00151, 2.01703, + 2.03234, 2.04716, 2.06082, 2.07363, 2.08461, 2.09386, 2.10143, + 2.10764, 2.11283, 2.11671, 2.11938, 2.12125, 2.1219, 2.12723, + 2.12654, 2.12621, 2.12561, 2.12494, 2.12093]) +_DNC1 = np.array([ + 0.0, -0.000435022, -0.000479481, -0.000531558, -0.000622448, + -0.000660866, -0.000693492, -0.000718251, -0.000732869, -0.000735755, + -0.000744294, -0.000761493, -0.000774238, -0.00078392, -0.000788939, + -0.00080946, -0.000839848, -0.000845825, -0.000874337, -0.000890074, + -0.00089873, -0.000908778, -0.000920012, -0.000932184, -0.000959514, + -0.000974043, -0.000988264, -0.00100258, -0.00101634, -0.00102762, + -0.00103757, -0.00104337, -0.00104563, -0.00104458, -0.00104144, + -0.00103719, -0.00103089, -0.00102262, -0.00101355, -0.00100249, + -0.00100934, -0.000998299, -0.000990961, -0.000985845, -0.000984529, + -0.000989315]) + + +def _goffgratch_svp_water(temp): + """Goff-Gratch (1946) saturation vapor pressure over water (Pa). + + ``wv_sat_methods.F90:569-580`` (``GoffGratch_svp_water``, the scalar + form — the vectorised variant splits the log differently), + ``tboil = 373.16`` (wv_saturation.F90:87). + """ + return 10.0 ** ( + -7.90298 * (_TBOIL / temp - 1.0) + + 5.02808 * jnp.log10(_TBOIL / temp) + - 1.3816e-7 * (10.0 ** (11.344 * (1.0 - temp / _TBOIL)) - 1.0) + + 8.1328e-3 * (10.0 ** (-3.49149 * (_TBOIL / temp - 1.0)) - 1.0) + + jnp.log10(1013.246) + ) * 100.0 + + +def _qsat_water_cam(temp, pres): + """CAM saturation specific humidity over liquid water (kg/kg). + + :func:`_goffgratch_svp_water`, then ``wv_sat_svp_to_qsat`` + (wv_sat_methods.F90:185-198): ``qs = 1`` when ``p - es <= 0``, else + ``epsilo*es / (p - omeps*es)``. See the module docstring for why this + is NOT :func:`mam4_jax.physics.saturation.qsat_water`. + """ + es = _goffgratch_svp_water(temp) + saturated = (pres - es) <= 0.0 + safe_den = jnp.where(saturated, 1.0, pres - _OMEPS * es) + return jnp.where(saturated, 1.0, _EPSILO * es / safe_den) + + +def calc_h2so4_wtpct(temp, pres, qh2o): + """Weight % H2SO4 of sulfate aerosol (25-100). + + Port of ``calc_h2so4_wtpct`` (modal_aero_wateruptake.F90:1087-1171), + Tabazadeh et al. (GRL 1997). Water activity ``qh2o / qsat_water`` selects + one of three coefficient sets (< 0.05, 0.05-0.85, > 0.85); the low set + clamps activity up to 1e-6, the high set down to 1.0. Each branch is + evaluated on the activity clipped into that branch's domain, so the + selected branch reproduces the Fortran exactly and the dead branches + stay finite (reverse-mode safe). + + Note the temperature interpolation ``(temp - 190)/70`` uses the RAW + ``temp`` argument — the [140, 450] K clamp lives in the CALLER + (:func:`calc_h2so4_equilib_mixrat`), matching the Fortran. + """ + qs = _qsat_water_cam(temp, pres) + activ = qh2o / qs + + low = activ < 0.05 + high = activ > 0.85 + # Per-branch activity, clipped into the branch's own domain. Inside the + # selected branch the clip reduces to the Fortran's own clamps + # (max(activ, 1e-6) low, min(activ, 1) high, identity mid). + a_lo = jnp.clip(activ, 1.0e-6, 0.05) + a_mid = jnp.clip(activ, 0.05, 0.85) + a_hi = jnp.clip(activ, 0.85, 1.0) + + def _cont(a, atab, btab, ctab, dtab): + return atab * a ** btab + ctab * a + dtab + + contl = jnp.where( + low, _cont(a_lo, 12.37208932, -0.16125516114, + -30.490657554, -2.1133114241), + jnp.where( + high, _cont(a_hi, -180.06541028, -0.38601102592, + -93.317846778, 273.88132245), + _cont(a_mid, 11.820654354, -0.20786404244, + -4.807306373, -5.1727540348))) + conth = jnp.where( + low, _cont(a_lo, 13.455394705, -0.1921312255, + -34.285174607, -1.7620073078), + jnp.where( + high, _cont(a_hi, -176.95814097, -0.36257048154, + -90.469744201, 267.45509988), + _cont(a_mid, 12.891938068, -0.23233847708, + -6.4261237757, -4.9005471319))) + + contt = contl + (conth - contl) * ((temp - 190.0) / 70.0) + conwtp = contt * 98.0 + 1000.0 + wtpct = (100.0 * contt * 98.0) / conwtp + return jnp.clip(wtpct, 25.0, 100.0) + + +def _knot_index(knots, w, start): + """0-based upper-knot index for the Fortran ``do while`` table walk. + + ``i = start; do while (w > knots(i)) i = i + 1`` (1-based) exits at the + first ``i >= start`` with ``knots(i) >= w`` — i.e. ``searchsorted`` + (side='left') floored at ``start``. ``w`` is always <= 100 = the last + knot, so no upper clip is needed; one is applied anyway for safety. + """ + idx = jnp.searchsorted(jnp.asarray(knots), w, side="left") + return jnp.clip(idx, start, len(knots) - 1) + + +def _surf_tension_flat(wtpct_flat, t): + """First surface-tension lookup (F90:995-1005): value at ``wtpct_flat`` + plus the d(sigma)/d(wt%) slope. Preserves the upstream abscissa + mismatch — see the module docstring.""" + i = _knot_index(_STWTP, wtpct_flat, 1) + sig1 = jnp.asarray(_STC0)[i - 1] + jnp.asarray(_STC1)[i - 1] * t + sig2 = jnp.asarray(_STC0)[i] + jnp.asarray(_STC1)[i] * t + dsigma_dwt = (sig2 - sig1) / (jnp.asarray(_STWTP)[i] + - jnp.asarray(_STWTP)[i - 1]) + # Faithful: sig1 belongs to knot i-1 but the offset is from knot i. + surf_tens = sig1 + dsigma_dwt * (wtpct_flat - jnp.asarray(_STWTP)[i]) + return surf_tens, dsigma_dwt + + +def _density_flat(wtpct_flat, t): + """First density lookup (F90:1008-1018): value + d(rho)/d(wt%).""" + i = _knot_index(_DNWTP, wtpct_flat, 5) + den1 = jnp.asarray(_DNC0)[i - 1] + jnp.asarray(_DNC1)[i - 1] * t + den2 = jnp.asarray(_DNC0)[i] + jnp.asarray(_DNC1)[i] * t + drho_dwt = (den2 - den1) / (jnp.asarray(_DNWTP)[i] + - jnp.asarray(_DNWTP)[i - 1]) + density = den1 + drho_dwt * (wtpct_flat - jnp.asarray(_DNWTP)[i - 1]) + return density, drho_dwt + + +def _surf_tension_mode(wtpct, t): + """Second surface-tension lookup (F90:1026-1036), correct ``frac`` form.""" + i = _knot_index(_STWTP, wtpct, 1) + sig1 = jnp.asarray(_STC0)[i - 1] + jnp.asarray(_STC1)[i - 1] * t + sig2 = jnp.asarray(_STC0)[i] + jnp.asarray(_STC1)[i] * t + frac = (jnp.asarray(_STWTP)[i] - wtpct) / (jnp.asarray(_STWTP)[i] + - jnp.asarray(_STWTP)[i - 1]) + return sig1 * frac + sig2 * (1.0 - frac) + + +def _density_mode(wtpct, t): + """Second density lookup (F90:1039-1047), correct ``frac`` form.""" + i = _knot_index(_DNWTP, wtpct, 5) + den1 = jnp.asarray(_DNC0)[i - 1] + jnp.asarray(_DNC1)[i - 1] * t + den2 = jnp.asarray(_DNC0)[i] + jnp.asarray(_DNC1)[i] * t + frac = (jnp.asarray(_DNWTP)[i] - wtpct) / (jnp.asarray(_DNWTP)[i] + - jnp.asarray(_DNWTP)[i - 1]) + return den1 * frac + den2 * (1.0 - frac) + + +def calc_h2so4_equilib_mixrat(temp, pres, qh2o, dmean): + """Equilibrium H2SO4 mixing ratio over sulfate particles. + + Port of ``calc_h2so4_equilib_mixrat`` + (modal_aero_wateruptake.F90:895-1083). Sequence: + + 1. Clamp T to [140, 450] K; flat-surface composition ``wtpct_flat`` + via :func:`calc_h2so4_wtpct`. + 2. Kelvin factor for WATER over the particle (from the flat-surface + surface tension/density and their wt% derivatives); recompute the + composition at the Kelvin-reduced water, floored at ``wtpct_flat``. + 3. Giauque (1959) enthalpy fit at that composition (floored at 0). + 4. Ayers (1980) pure-H2SO4 equilibrium vapor pressure with the + Kulmala (1990) temperature correction, composition-adjusted by the + enthalpy term; converted atm -> Pa -> mol/mol. + 5. Kelvin factor for H2SO4 (mode surface tension/density at the + adjusted composition), exponent clamped to +/-100. + + Parameters + ---------- + temp : temperature (K) + pres : pressure (Pa) + qh2o : water vapor specific humidity (kg/kg) + dmean : mean particle diameter of the mode (m) — CAM passes + ``dgncur_awet * exp(1.5*alnsg**2)``, the wet surface-mode mean + diameter of the PREVIOUS step (the lagged carried state, plan 024 + §6). + + Returns + ------- + (qh2so4_equilib, wtpct, sulden) : + equilibrium H2SO4 mixing ratio (mol/mol), sulfate composition + (weight % H2SO4), sulfate density (g/cm3). + """ + t = jnp.clip(temp, 140.0, 450.0) + + wtpct_flat = calc_h2so4_wtpct(t, pres, qh2o) + + surf_tens, dsigma_dwt = _surf_tension_flat(wtpct_flat, t) + sulfate_density, drho_dwt = _density_flat(wtpct_flat, t) + + r = dmean * 100.0 / 2.0 # mode radius (cm) from diameter (m) + + # Kelvin effect for water (F90:1021-1029) + rkelvin_h2o_b = (1.0 + wtpct_flat * drho_dwt / sulfate_density + - 3.0 * wtpct_flat * dsigma_dwt / (2.0 * surf_tens)) + rkelvin_h2o_a = (2.0 * _WTMOL_H2SO4 * surf_tens + / (sulfate_density * _RGAS_CGS * t * r)) + rkelvin_h2o = jnp.exp(rkelvin_h2o_a * rkelvin_h2o_b) + + qh2o_kelvin = qh2o / rkelvin_h2o + wtpct = calc_h2so4_wtpct(t, pres, qh2o_kelvin) + wtpct = jnp.maximum(wtpct, wtpct_flat) + + # Giauque (1959) enthalpy fit (F90:1050-1052) + en = 4.184 * (23624.8 + - 1.14208e8 / ((wtpct - 105.318) ** 2 + 4798.69)) + en = jnp.maximum(en, 0.0) + + surf_tens_mode = _surf_tension_mode(wtpct, t) + sulden = _density_mode(wtpct, t) + + # Ayers (1980) + Kulmala (1990) correction (F90:1055-1075) + fk4 = 1.0 + jnp.log(_T0_KULM / t) - _T0_KULM / t + factor_kulm = -1.0 / t + _FK2 + _FK3 * fk4 + sulfequil = _FK0 + 10156.0 * factor_kulm - en / (8.3143 * t) + sulfequil = jnp.exp(sulfequil) * 1.01325e5 / pres # atm -> Pa -> mol/mol + + # Kelvin curvature factor for H2SO4 (F90:1077-1082) + akelvin = (2.0 * _WTMOL_H2SO4 * surf_tens_mode + / (t * sulden * _RGAS_CGS)) + expon = jnp.clip(akelvin / r, -100.0, 100.0) + qh2so4_equilib = sulfequil * jnp.exp(expon) + + return qh2so4_equilib, wtpct, sulden + + +def h2so4_reversible_uptake(qgas_h2so4, qaer_so4, uptkratebb, sulfeq, + deltat, ido_so4a): + """Per-mode so4 tendencies from REVERSIBLE H2SO4 uptake (mol/mol/s). + + Port of the stratospheric (``associated(sulfeq) .and. k <= troplev``) + branch of CAM's gasaerexch (modal_aero_gasaerexch.F90:523-566) — the + consumer of :func:`calc_h2so4_equilib_mixrat`. Where the tropospheric + branch condenses irreversibly (``dqdt = fgain*q_gas*avg_uprt``), this + one relaxes the gas toward the mode-weighted equilibrium and lets + over-saturated modes EVAPORATE:: + + kxt = dtxx * sum_n(uptk_n) (active modes) + pxt = max(0, dtxx * sum_n(uptk_n * sulfeq_n)) + g_equ = pxt / kxt + g_avg = g_equ + (g_bgn - g_equ) * (1 - exp(-kxt)) / kxt + (first-order form g_bgn*(1 - kxt/2) + pxt/2 for kxt < 1e-5) + a_end(n) = max(0, a_bgn(n) + dtxx * uptk_n * (g_avg - sulfeq_n)) + dqdt(n) = (a_end(n) - a_bgn(n)) / dtxx + + with ``dtxx = deltat * (1 + 1e-15)`` (the Fortran's :392 nudge, applied + here so callers pass the plain ``deltat``). + + ``ido_so4a`` mirrors the Fortran mode classification: ``1`` = the mode + carries an so4 tracer (``a_bgn`` read from ``qaer_so4``), ``2`` = the + mode condenses but has no so4 slot (``a_bgn = 0`` — CAM's pcarbon + age-source mode; the driver routes its uptake through the age pair), + ``0`` = inactive (zero tendency, excluded from every sum). + + Deviation from Fortran arithmetic, repo-standard (see plan 026 / + ADR-019): ``1 - exp(-kxt)`` is written ``-expm1(-kxt)``. At the branch + threshold ``kxt = 1e-5`` the forms differ by ~2e-11 relative — the + test gates the transcribed-Fortran form at exactly that level. + + All array arguments broadcast; the mode axis is LAST. Returns + ``(dqdt_so4, sum_dqdt_so4)``. + """ + dtxx = deltat * (1.0 + 1.0e-15) + active = jnp.asarray(ido_so4a) > 0 + has_slot = jnp.asarray(ido_so4a) == 1 + + uptk = jnp.where(active, uptkratebb, 0.0) + kxt = dtxx * jnp.sum(uptk, axis=-1) + pxt = jnp.maximum(0.0, dtxx * jnp.sum(uptk * sulfeq, axis=-1)) + + g_bgn = qgas_h2so4 + # Exponential decay toward equilibrium; g_equ = pxt/kxt is guarded on + # the small-kxt branch (double-where — a masked 0/0 still poisons + # reverse-mode cotangents). + big = kxt >= 1.0e-5 + safe_kxt = jnp.where(big, kxt, 1.0) + g_equ = pxt / safe_kxt + g_avg_big = g_equ + (g_bgn - g_equ) * (-jnp.expm1(-safe_kxt)) / safe_kxt + g_avg_small = g_bgn * (1.0 - 0.5 * kxt) + 0.5 * pxt + g_avg = jnp.where(big, g_avg_big, g_avg_small) + + a_bgn = jnp.where(has_slot, qaer_so4, 0.0) + a_end = jnp.maximum( + 0.0, a_bgn + dtxx * uptk * (g_avg[..., None] - sulfeq)) + dqdt = jnp.where(active, (a_end - a_bgn) / dtxx, 0.0) + return dqdt, jnp.sum(dqdt, axis=-1) diff --git a/mam4_jax/physics/wateruptake.py b/mam4_jax/physics/wateruptake.py index 169664e..8d6d81f 100644 --- a/mam4_jax/physics/wateruptake.py +++ b/mam4_jax/physics/wateruptake.py @@ -66,6 +66,33 @@ _H2OMMR_IDX: int = 0 +class WateruptakeTables: + """Every mode/species table wateruptake reads, as one bundle. + + The default (`_E3SM_TABLES`, from the module constants above) keeps + the E3SM path bit-identical; the CAM driver builds instances from a + `Topology` with indices in its own state coordinate (plan 025 G4b). + """ + + def __init__(self, *, lmassptr, slot_valid, per_slot_density, + per_slot_hygro, sigmag, rhcrystal, rhdeliques): + self.lmassptr = np.asarray(lmassptr) + self.slot_valid = np.asarray(slot_valid) + self.per_slot_density = np.asarray(per_slot_density) + self.per_slot_hygro = np.asarray(per_slot_hygro) + self.sigmag = np.asarray(sigmag) + self.rhcrystal = np.asarray(rhcrystal) + self.rhdeliques = np.asarray(rhdeliques) + + +_E3SM_TABLES = WateruptakeTables( + lmassptr=INDEX_TABLES.lmassptr_amode, slot_valid=SLOT_VALID, + per_slot_density=PER_SLOT_DENSITY, per_slot_hygro=PER_SLOT_HYGRO, + sigmag=SIGMAG_AMODE, rhcrystal=RHCRYSTAL_AMODE, + rhdeliques=RHDELIQUES_AMODE, +) + + def _safe_div(numer, denom, floor: float, fallback): """Return ``numer / denom`` where ``denom > floor``, else ``fallback``. @@ -77,12 +104,42 @@ def _safe_div(numer, denom, floor: float, fallback): return jnp.where(denom > floor, numer / safe_denom, fallback) -def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, Any]: +def wateruptake(state: dict[str, Any], params=None, config=None, + *, tables: WateruptakeTables | None = None, + qv=None, strat=None) -> dict[str, Any]: """Compute aerosol equilibrium water uptake. ADR-009 entry point. See module docstring for the ``state`` dict contract. + + ``tables``: mode/species tables; ``None`` (default) = the E3SM + MAM4-MOM constants — bit-identical to the pre-parameter behaviour. + ``qv``: water-vapor mass mixing ratio; ``None`` (default) reads + ``q[..., 0]`` (the E3SM box contract, where slot 0 is Q). The CAM + driver keeps water vapor OUTSIDE its aerosol window and passes it + explicitly. + + ``strat``: CAM's stratospheric-sulfate water uptake + (``modal_aero_wateruptake_sub``'s ``modal_strat_sulfate .and. + k < troplev`` branch, CESM3 modal_aero_wateruptake.F90:583-591 — + the box driver sets its tropopause above the single level, so under + ``strat`` the branch is live EVERYWHERE). ``None`` (default) = the + Köhler + hysteresis path only, bit-identical to before. Otherwise a + dict with: + + * ``so4_slot``: per-mode slot index of the so4 species on the slot + axis (−1 = mode has none; its ``so4dryvol`` is then 0 and the + formula collapses to a dry particle); + * ``so4specdens``: sulfate density (kg/m³); + * ``wtpct``, ``sulden``: (..., nmodes) — the Tabazadeh composition + (weight % H2SO4) and solution density (g/cm³) from + :func:`mam4_jax.physics.strat_sulfate.calc_h2so4_equilib_mixrat`. + + The wet volume is then solution volume from the wt% composition: + ``(dryvol − so4dryvol) + so4dryvol·ρ_so4/(sulden·wtpct·10)``, floored + at ``dryvol`` — no Köhler, no hysteresis (upstream behaviour). """ - del params, config # All constants live in mam4_jax.core.data / .constants. + del params, config + tb = _E3SM_TABLES if tables is None else tables q = jnp.asarray(state["q"], dtype=jnp.float64) dgncur_a = jnp.asarray(state["dgncur_a"], dtype=jnp.float64) @@ -98,17 +155,17 @@ def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, An # For unused slots (lmassptr_amode == -1) we use index 0 then zero out # the result via SLOT_VALID — this keeps every contribution but ignores # unused species. - lmass_idx = jnp.asarray(INDEX_TABLES.lmassptr_amode, dtype=jnp.int32) - safe_idx = jnp.where(jnp.asarray(SLOT_VALID), lmass_idx, 0) - slot_mask = jnp.asarray(SLOT_VALID, dtype=jnp.float64) + lmass_idx = jnp.asarray(tb.lmassptr, dtype=jnp.int32) + safe_idx = jnp.where(jnp.asarray(tb.slot_valid), lmass_idx, 0) + slot_mask = jnp.asarray(tb.slot_valid, dtype=jnp.float64) # raer[..., m, s]: contribution of species (m, s) to mode m, zeroed # for invalid slots so the sums below are unaffected. q_gathered = jnp.take(q, safe_idx, axis=-1) # (..., m, s) raer = q_gathered * slot_mask # (..., m, s) - per_slot_density = jnp.asarray(PER_SLOT_DENSITY) # (m, s) - per_slot_hygro = jnp.asarray(PER_SLOT_HYGRO) # (m, s) + per_slot_density = jnp.asarray(tb.per_slot_density) # (m, s) + per_slot_hygro = jnp.asarray(tb.per_slot_hygro) # (m, s) # Mass / dry-volume / volume-weighted hygro per mode. maer = jnp.sum(raer, axis=-1) # (..., m) @@ -124,7 +181,7 @@ def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, An hygro = _safe_div(hygro_volwgt, dryvolmr, 1.0e-30, spechygro_1) # (..., m) # Per-mode geometric quantities (Fortran lines 310–326). - sigmag = jnp.asarray(SIGMAG_AMODE) # (m,) + sigmag = jnp.asarray(tb.sigmag) # (m,) alnsg = jnp.log(sigmag) v2ncur_a = 1.0 / ((_PI / 6.0) * dgncur_a ** 3 * jnp.exp(4.5 * alnsg ** 2)) # (..., m) @@ -138,7 +195,7 @@ def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, An # Step 2 — relative humidity (Fortran lines 333–362). # --------------------------------------------------------------------- - h2ommr = q[..., _H2OMMR_IDX] + h2ommr = q[..., _H2OMMR_IDX] if qv is None else jnp.asarray(qv) qs = qsat_water(t, pmid) rh = jnp.where(qs > h2ommr, h2ommr / jnp.maximum(qs, 1e-30), 0.98) @@ -174,8 +231,8 @@ def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, An # rh < rhcrystal → collapse to dry # rhcrystal ≤ rh < rhdeliques → linear interpolation # rh ≥ rhdeliques → use the Köhler result as-is - rhcrystal = jnp.asarray(RHCRYSTAL_AMODE) - rhdeliques = jnp.asarray(RHDELIQUES_AMODE) + rhcrystal = jnp.asarray(tb.rhcrystal) + rhdeliques = jnp.asarray(tb.rhdeliques) hystfac = 1.0 / jnp.maximum(1.0e-5, rhdeliques - rhcrystal) below_crystal = rh_pm < rhcrystal @@ -193,6 +250,30 @@ def wateruptake(state: dict[str, Any], params=None, config=None) -> dict[str, An wetrad = jnp.where(below_crystal, dryrad, jnp.where(in_hysteresis, wetrad_h, wetrad_q)) + if strat is not None: + # CAM stratospheric-sulfate water (see docstring). so4dryvol is + # the single-particle so4 dry volume, calcsize's normalisation + # (modal_aero_calcsize.F90:1571-1576): + # so4dryvol = dryvol * so4dryvolmr/dryvolmr (0 below 1e-31) + so4_slot = np.asarray(strat["so4_slot"]) + nmode = raer.shape[-1] if raer.ndim == 2 else raer.shape[-2] + so4dryvolmr = jnp.zeros_like(dryvolmr) + for m in range(len(so4_slot)): + if so4_slot[m] >= 0: + so4dryvolmr = so4dryvolmr.at[..., m].set( + jnp.maximum(raer[..., m, int(so4_slot[m])], 0.0) + / strat["so4specdens"]) + safe_dvmr = jnp.where(dryvolmr > 1.0e-31, dryvolmr, 1.0) + so4dryvol = jnp.where(so4dryvolmr > 1.0e-31, + dryvol * so4dryvolmr / safe_dvmr, 0.0) + wetvol_s = ((dryvol - so4dryvol) + + so4dryvol * strat["so4specdens"] + / (jnp.asarray(strat["sulden"]) + * jnp.asarray(strat["wtpct"]) * 10.0)) + wetvol = jnp.maximum(wetvol_s, dryvol) + wetrad = jnp.maximum((wetvol / _PI43) ** _THIRD, dryrad) + wtrvol = jnp.maximum(wetvol - dryvol, 0.0) + # Outputs (Fortran lines 469–476). dgncur_awet = dgncur_a * (wetrad / dryrad) qaerwat = RHOH2O * naer * wtrvol diff --git a/scripts/plot_cam_vs_e3sm.py b/scripts/plot_cam_vs_e3sm.py new file mode 100644 index 0000000..12f41c2 --- /dev/null +++ b/scripts/plot_cam_vs_e3sm.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python3 +"""CAM vs E3SM: where the two MAM code lines actually differ, and by how much. + +Three panels, each answering a question that came up porting CAM's kernels: + + 1. Rename: how far apart are the two algorithms, and where? + 2. Rename: is the CAM branch right? (against CAM's own Fortran) + 3. Condensation: is the tropospheric H2SO4 path the same maths? + +Data from /tmp/camfig/data.json (see the generator in the commit that added +this). Writes docs/figures/cam_vs_e3sm.png. +""" +from __future__ import annotations + +import json +from pathlib import Path + +import matplotlib +matplotlib.use("Agg") +import matplotlib.pyplot as plt +import numpy as np + +D = json.loads(Path("/tmp/camfig/data.json").read_text()) +OUT = Path(__file__).resolve().parent.parent / "docs" / "figures" / "cam_vs_e3sm.png" + +# Validated categorical palette (dataviz reference instance, light mode): +# node scripts/validate_palette.js "#2a78d6,#eb6834,#1baf7a,#eda100" --mode light +# -> ALL CHECKS PASS +BLUE, ORANGE, AQUA = "#2a78d6", "#eb6834", "#1baf7a" +SURFACE, INK, INK2, GRID = "#fcfcfb", "#0b0b0b", "#52514e", "#e3e3e0" + +plt.rcParams.update({ + "figure.facecolor": SURFACE, "axes.facecolor": SURFACE, + "axes.edgecolor": GRID, "axes.labelcolor": INK2, "text.color": INK, + "xtick.color": INK2, "ytick.color": INK2, + "axes.grid": True, "grid.color": GRID, "grid.linewidth": 0.6, + "axes.spines.top": False, "axes.spines.right": False, + "font.size": 9, "axes.titlesize": 10, "axes.titlepad": 8, + "lines.linewidth": 2.0, "legend.frameon": False, "legend.fontsize": 8, +}) + +fig, ax = plt.subplots(1, 3, figsize=(15.5, 5.4)) +fig.suptitle("CAM vs E3SM — where the two MAM code lines diverge", + fontsize=13, x=0.008, ha="left", y=0.975) +fig.text(0.008, 0.925, + "JAX port validated against CAM cam6_4_187 via mam-box-fortran · " + "aitken→accum rename, and tropospheric H2SO4 condensation", + fontsize=8.5, color=INK2, ha="left") + +# ---- 1. rename: transfer fraction vs growth -------------------------------- +p = D["p1"]; g = np.asarray(p["growths"]) +a = ax[0] +a.plot(g, p["cam_1.2e-7"], color=BLUE, label="CAM") +a.plot(g, p["e3sm_1.2e-7"], color=ORANGE, label="E3SM") +a.plot(g, p["cam_9e-8"], color=BLUE, ls=(0, (5, 3)), lw=1.6) +a.plot(g, p["e3sm_9e-8"], color=ORANGE, ls=(0, (5, 3)), lw=1.6) +a.set_xscale("log"); a.set_yscale("log") +a.text(0.03, 0.96, "solid: dgn_old = 1.2e-7 m\ndashed: dgn_old = 9e-8 m", + transform=a.transAxes, fontsize=8, color=INK2, va="top") +a.annotate("E3SM skips CAM's up-front growth gate,\nso it transfers where CAM does nothing", + xy=(g[1], p["e3sm_1.2e-7"][1]), xytext=(0.05, 0.16), + textcoords="axes fraction", fontsize=8, color=ORANGE, weight="bold", + arrowprops=dict(arrowstyle="-", color=ORANGE, lw=0.8)) +a.annotate("converge once growth pushes\ndgn_new past dp_cut", + xy=(g[-3], p["cam_1.2e-7"][-3]), xytext=(0.42, 0.60), + textcoords="axes fraction", fontsize=8, color=INK2, + arrowprops=dict(arrowstyle="-", color=INK2, lw=0.8)) +a.set_title("1 · Rename: up to 4.3× apart, and only in a window", loc="left") +a.set_xlabel("fractional growth of the aitken mode over the step") +a.set_ylabel("fraction of aitken number transferred") +a.legend(loc="lower right") + +# ---- 2. rename: CAM branch vs CAM's Fortran -------------------------------- +p2 = D["p2"]; dgs = np.asarray(p2["dgns"]) * 1e9 +a = ax[1] +a.plot(dgs, p2["cam_0.01"], color=BLUE, label="CAM (JAX port)") +a.plot(dgs, p2["e3sm_0.01"], color=ORANGE, label="E3SM (JAX port)") +ref = D["ref"] +rx = [r["dgn_old"] * 1e9 for r in ref if r["growth"] == 0.01] +ry = [r["xferfrac_num"] for r in ref if r["growth"] == 0.01] +a.plot(rx, ry, "o", ms=11, mfc="none", mec=INK, mew=2.0, ls="none", + label="CAM Fortran (reference)") +a.axvline(p2["dp_cut"] * 1e9, color=INK2, lw=0.9, ls=(0, (4, 3))) +a.text(0.50, 0.40, f"dp_cut = {p2['dp_cut']*1e9:.1f} nm", + transform=a.transAxes, fontsize=8, color=INK2) +a.annotate("the port sits on the reference\nto 8.1e-15 — machine precision", + xy=(rx[0], ry[0]), xytext=(0.42, 0.12), textcoords="axes fraction", + fontsize=8, color=INK, weight="bold", + arrowprops=dict(arrowstyle="-", color=INK, lw=0.8)) +a.set_xscale("log"); a.set_yscale("log") +a.set_title("2 · The CAM branch is right, the E3SM one is not", loc="left") +a.set_xlabel("aitken dgn before growth (nm), growth = 1 %") +a.set_ylabel("fraction of aitken number transferred") +a.legend(loc="upper left") + +# ---- 3. condensation equivalence ------------------------------------------- +errs = np.asarray(D["p3"]["errs"]) +a = ax[2] +a.hist(errs, bins=np.logspace(-17, -12, 34), color=AQUA, edgecolor=SURFACE, lw=0.6) +a.set_xscale("log") +a.axvline(np.finfo(np.float64).eps, color=INK2, lw=0.9, ls=(0, (4, 3))) +a.text(0.30, 0.96, "1 machine ε", transform=a.transAxes, + fontsize=8, color=INK2, va="top") +a.text(0.40, 0.82, + f"400 random cases, worst {errs.max():.2e}\n\n" + "CAM's fgain + avg_uprt formulation and\nthe JAX closed form are the same\n" + "competing-sink ODE — not an\napproximation, identical.", + transform=a.transAxes, fontsize=8, color=INK2, va="top") +a.set_title("3 · Condensation: the same maths, to round-off", loc="left") +a.set_xlabel("relative difference, CAM formula vs JAX closed form") +a.set_ylabel("cases") + +fig.tight_layout(rect=(0, 0.005, 1, 0.90)) +OUT.parent.mkdir(parents=True, exist_ok=True) +fig.savefig(OUT, dpi=170) +print(f"wrote {OUT}") +print(f" condensation worst err : {errs.max():.3e}") +print(f" rename ref points : {len(ref)}") diff --git a/tests/reference/cam_box/README.md b/tests/reference/cam_box/README.md new file mode 100644 index 0000000..07b6267 --- /dev/null +++ b/tests/reference/cam_box/README.md @@ -0,0 +1,25 @@ +# CAM box-model reference trajectories + +Generated from `mam-box-fortran` **fixdumfac** builds (the JAX calcsize +uses the correct per-mode `dumfac` by default; the non-fixdumfac builds +reproduce upstream CAM's stale-scalar bug — see +`mam-box-fortran/docs/bugs/BUG-cam-calcsize-stale-dumfac.md` and +`calcsize(bug_compat_stale_dumfac=True)`): + + cd mam-box-fortran + ./build/build_cam.sh --fix-dumfac + ./build/build_cam.sh --fix-dumfac --mam5 + build/cam-mam4-fixdumfac/mam_box_cam.exe 0.9 nostrat 30 120 all mam4 no_acc_crs + build/cam-mam4-fixdumfac/mam_box_cam.exe 0.9 strat 30 120 all mam4 no_acc_crs + build/cam-mam5-fixdumfac/mam_box_cam.exe 0.9 nostrat 30 120 all mam5 no_acc_crs + build/cam-mam5-fixdumfac/mam_box_cam.exe 0.9 strat 30 120 all mam5 no_acc_crs + +(each run writes `mam_box_cam.out` in its cwd; the four are committed +here as `_.out`). Namelist: all defaults (T=273 K, p=1e5 Pa, +RH=0.9, dt=30 s, 120 steps, numc = 1e8/1e9/1e5/1 (+1e4 mode 5), so4frac +1/1/1/0, qso2=1e-7, qh2so4=1e-11 vmr, SO2→H2SO4 1e-5 /s). + +Columns are `es14.6` — SEVEN significant digits — except `totS_mol` +(`es24.16`, full precision). Per-tracer comparisons therefore bottom out +at ~5e-7 relative (the print floor); `totS` is the machine-precision +handle and agrees with the JAX driver at ~4.5e-15 on all four runs. diff --git a/tests/reference/cam_box/mam4_nostrat.out b/tests/reference/cam_box/mam4_nostrat.out new file mode 100644 index 0000000..c9b7a39 --- /dev/null +++ b/tests/reference/cam_box/mam4_nostrat.out @@ -0,0 +1,121 @@ +#step num_a1 num_a2 num_a3 so4_a1 so4_a2 so4_a3 h2so4 dgn_a1 dgnwet_a1 wetdens_a1 so2 totS_mol num_a5 so4_a5 + 1 7.888318E+07 7.253410E+10 7.836255E+04 4.608142E-10 1.900591E-10 2.750395E-09 1.316848E-14 1.100000E-07 1.942354E-07 1.139857E+03 2.211061E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 2 7.888302E+07 7.781456E+10 7.836255E+04 4.627754E-10 2.152252E-10 2.750478E-09 7.836156E-11 1.100157E-07 1.942635E-07 1.139856E+03 2.210397E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 3 7.888285E+07 1.611556E+11 7.836255E+04 4.662347E-10 4.226948E-10 2.750626E-09 1.546190E-14 1.101716E-07 1.945439E-07 1.139845E+03 2.209734E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 4 7.888269E+07 1.633421E+11 7.836255E+04 4.680815E-10 4.573792E-10 2.750703E-09 7.029511E-11 1.104455E-07 1.950364E-07 1.139826E+03 2.209072E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 5 7.888252E+07 2.305016E+11 7.836255E+04 4.711837E-10 6.556868E-10 2.750834E-09 1.272256E-14 1.105912E-07 1.952984E-07 1.139816E+03 2.208409E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 6 7.888235E+07 2.298260E+11 7.836255E+04 4.729310E-10 6.983566E-10 2.750907E-09 6.351650E-11 1.108351E-07 1.957369E-07 1.139799E+03 2.207747E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 7 7.888219E+07 2.842577E+11 7.836255E+04 4.757442E-10 8.889421E-10 2.751025E-09 1.062361E-14 1.109720E-07 1.959831E-07 1.139790E+03 2.207084E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 8 7.888202E+07 2.812544E+11 7.836255E+04 4.774044E-10 9.387872E-10 2.751094E-09 5.741764E-11 1.111917E-07 1.963780E-07 1.139775E+03 2.206422E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 9 7.888186E+07 2.991948E+11 7.836255E+04 4.799727E-10 1.064404E-09 2.751200E-09 4.942616E-11 1.113209E-07 1.966105E-07 1.139766E+03 2.205760E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 10 7.888169E+07 3.008383E+11 7.836255E+04 4.823525E-10 1.157434E-09 2.751299E-09 6.933812E-11 1.115203E-07 1.969689E-07 1.139752E+03 2.205099E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 11 7.888152E+07 3.182477E+11 7.836255E+04 4.850038E-10 1.300310E-09 2.751408E-09 4.650646E-11 1.117044E-07 1.972999E-07 1.139740E+03 2.204437E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 12 7.888136E+07 3.161120E+11 7.836255E+04 4.872430E-10 1.394306E-09 2.751500E-09 6.566004E-11 1.119087E-07 1.976674E-07 1.139726E+03 2.203776E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 13 7.888119E+07 3.170520E+11 7.836255E+04 4.897349E-10 1.509923E-09 2.751602E-09 6.613646E-11 1.120808E-07 1.979767E-07 1.139715E+03 2.203115E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 14 7.888103E+07 3.155634E+11 7.836255E+04 4.921913E-10 1.624700E-09 2.751702E-09 6.733001E-11 1.122716E-07 1.983199E-07 1.139702E+03 2.202454E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 15 7.888086E+07 3.136892E+11 7.836255E+04 4.946263E-10 1.743059E-09 2.751801E-09 6.546032E-11 1.124591E-07 1.986570E-07 1.139689E+03 2.201794E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 16 7.888070E+07 3.112521E+11 7.836255E+04 4.969972E-10 1.862359E-09 2.751897E-09 6.281619E-11 1.126443E-07 1.989900E-07 1.139677E+03 2.201133E-07 3.4808366689360348E-09 0.000000E+00 0.000000E+00 + 17 7.888053E+07 3.083019E+11 7.836255E+04 4.992959E-10 1.981802E-09 2.751990E-09 6.008326E-11 1.128241E-07 1.993133E-07 1.139665E+03 2.200473E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 18 7.888037E+07 3.049487E+11 7.836255E+04 5.015243E-10 2.101194E-09 2.752080E-09 5.742669E-11 1.129978E-07 1.996257E-07 1.139653E+03 2.199813E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 19 7.888021E+07 3.013127E+11 7.836255E+04 5.036863E-10 2.220516E-09 2.752167E-09 5.485810E-11 1.131658E-07 1.999277E-07 1.139642E+03 2.199153E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 20 7.888004E+07 2.975090E+11 7.836255E+04 5.057858E-10 2.339794E-09 2.752251E-09 5.235220E-11 1.133282E-07 2.002198E-07 1.139632E+03 2.198493E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 21 7.887988E+07 2.936423E+11 7.836255E+04 5.078259E-10 2.459054E-09 2.752332E-09 4.988539E-11 1.134855E-07 2.005027E-07 1.139621E+03 2.197834E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 22 7.887971E+07 2.897984E+11 7.836255E+04 5.098092E-10 2.578294E-09 2.752411E-09 4.745456E-11 1.136380E-07 2.007768E-07 1.139611E+03 2.197175E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 23 7.887955E+07 2.860326E+11 7.836255E+04 5.117380E-10 2.697477E-09 2.752487E-09 4.509117E-11 1.137858E-07 2.010426E-07 1.139602E+03 2.196516E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 24 7.887939E+07 2.823637E+11 7.836255E+04 5.136149E-10 2.816530E-09 2.752562E-09 4.285406E-11 1.139292E-07 2.013004E-07 1.139592E+03 2.195857E-07 3.4808366689360344E-09 0.000000E+00 0.000000E+00 + 25 7.887922E+07 2.787904E+11 7.836255E+04 5.154431E-10 2.935405E-09 2.752634E-09 4.078190E-11 1.140684E-07 2.015507E-07 1.139583E+03 2.195198E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 26 7.887906E+07 2.753097E+11 7.836255E+04 5.172260E-10 3.054097E-09 2.752704E-09 3.887570E-11 1.142037E-07 2.017939E-07 1.139575E+03 2.194540E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 27 7.887889E+07 2.719184E+11 7.836255E+04 5.189670E-10 3.172618E-09 2.752772E-09 3.712200E-11 1.143353E-07 2.020306E-07 1.139566E+03 2.193881E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 28 7.887873E+07 2.686136E+11 7.836255E+04 5.206690E-10 3.290985E-09 2.752838E-09 3.550479E-11 1.144635E-07 2.022611E-07 1.139558E+03 2.193223E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 29 7.887857E+07 2.653922E+11 7.836255E+04 5.223350E-10 3.409211E-09 2.752903E-09 3.400908E-11 1.145886E-07 2.024860E-07 1.139550E+03 2.192566E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 30 7.887840E+07 2.622516E+11 7.836255E+04 5.239672E-10 3.527309E-09 2.752967E-09 3.262169E-11 1.147107E-07 2.027057E-07 1.139542E+03 2.191908E-07 3.4808366689360340E-09 0.000000E+00 0.000000E+00 + 31 7.887824E+07 2.591888E+11 7.836255E+04 5.255679E-10 3.645291E-09 2.753029E-09 3.133122E-11 1.148302E-07 2.029205E-07 1.139534E+03 2.191250E-07 3.4808366689360336E-09 0.000000E+00 0.000000E+00 + 32 7.887808E+07 2.562014E+11 7.836255E+04 5.271390E-10 3.763167E-09 2.753090E-09 3.012785E-11 1.149471E-07 2.031307E-07 1.139527E+03 2.190593E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 33 7.887791E+07 2.532868E+11 7.836255E+04 5.286823E-10 3.880944E-09 2.753149E-09 2.900304E-11 1.150616E-07 2.033366E-07 1.139520E+03 2.189936E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 34 7.887775E+07 2.504425E+11 7.836255E+04 5.301994E-10 3.998629E-09 2.753208E-09 2.794938E-11 1.151738E-07 2.035384E-07 1.139512E+03 2.189279E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 35 7.887759E+07 2.476661E+11 7.836255E+04 5.316918E-10 4.116229E-09 2.753265E-09 2.696037E-11 1.152840E-07 2.037365E-07 1.139505E+03 2.188622E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 36 7.887742E+07 2.449555E+11 7.836255E+04 5.331608E-10 4.233748E-09 2.753322E-09 2.603030E-11 1.153921E-07 2.039309E-07 1.139499E+03 2.187966E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 37 7.887726E+07 2.423083E+11 7.836255E+04 5.346074E-10 4.351193E-09 2.753377E-09 2.515410E-11 1.154984E-07 2.041220E-07 1.139492E+03 2.187310E-07 3.4808366689360331E-09 0.000000E+00 0.000000E+00 + 38 7.887710E+07 2.397226E+11 7.836255E+04 5.360330E-10 4.468566E-09 2.753431E-09 2.432730E-11 1.156028E-07 2.043098E-07 1.139485E+03 2.186654E-07 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4.6000000000000000E+02, 1.0000000000000000E+05, 8.5999999999999999E-01, 1.0000000000000000E-08, 6.8513668116343774E-08, 4.8511330723621789E+01, 1.2623414486576272E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 8.5999999999999999E-01, 1.1000000000000001E-07, 5.6465248486593224E-10, 2.6587705572740212E+01, 1.0858391024784506E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 8.5999999999999999E-01, 8.9999999999999996E-07, 4.1549723870029595E-10, 2.5000000000000000E+01, 1.0747002999999999E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 9.4999999999999996E-01, 1.0000000000000000E-08, 3.5201400001629070E-08, 4.5504160373659886E+01, 1.2354209890394368E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 9.4999999999999996E-01, 1.1000000000000001E-07, 4.3516364187441945E-10, 2.5000000000000000E+01, 1.0747002999999999E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 9.4999999999999996E-01, 8.9999999999999996E-07, 4.1549723870029595E-10, 2.5000000000000000E+01, 1.0747002999999999E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 1.2000000000000000E+00, 1.0000000000000000E-08, 5.1665593769651063E-09, 3.6094500563203113E+01, 1.1561726214822967E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 1.2000000000000000E+00, 1.1000000000000001E-07, 4.3516364187441945E-10, 2.5000000000000000E+01, 1.0747002999999999E+00], +[ 4.6000000000000000E+02, 1.0000000000000000E+05, 1.2000000000000000E+00, 8.9999999999999996E-07, 4.1549723870029595E-10, 2.5000000000000000E+01, 1.0747002999999999E+00] +] +} diff --git a/tests/test_cam_coag.py b/tests/test_cam_coag.py new file mode 100644 index 0000000..3af695a --- /dev/null +++ b/tests/test_cam_coag.py @@ -0,0 +1,107 @@ +"""Validate the CAM coag port (coupling/cam_driver.py) — plan 025 G3. + +Reference: ``tests/reference/cam_coag/{mam4,mam5}.json`` from +``mam-box-fortran/tools/capture_coag`` — the REAL ``modal_aero_coag_sub`` +(cam6_4_187, ``pair_option_acoag = 3``) with prescribed diameters and wet +densities. 32 cases per topology: number-loading combinations that push +the three-branch closed forms through ``|tmpc| < 0.01``, ``|tmpa| < 0.001`` +and the general branch; pcarbon core 0 (saturated aging) vs 1e-11 pom +(fractional aging); aitken diameter ×2.5; warm/high-p vs cold/low-p. + +The getcoags kernel itself is byte-identical CAM-vs-E3SM and validated +elsewhere; what this pins is coag_sub's ORCHESTRATION (sequential number +solves consuming the prior mode's time-average, the combined aitken mass +transfer whose pcarbon-destined share ages straight through to accum +while accumulating shell volume, the legacy 8-monolayer aging fraction, +and the pcarbon direct+aging transfer). + +Found by this capture: ``shr_const_rgas`` is the PRODUCT +``6.02214e26 * 1.38065e-23 = 8314.467591`` — the rounded ``8314.46`` +shortcut is 9.1e-7 relative off, which the implicit number solves +amplified to ~2e-6 before the constant was corrected. + +Sliver rule as in test_cam_gasaerexch: post-transfer remnants below +1e-10 of the slot's own input are compared with a per-slot atol +(1e-13 × q_in), everything else at rtol 5e-13 (measured worst 6e-16). +""" +from __future__ import annotations + +import json +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_params import CAM_PARAMS +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +from mam4_jax.coupling.cam_driver import modal_aero_coag_cam + +REF_DIR = Path(__file__).resolve().parent / "reference" / "cam_coag" + + +def _load(tag): + with open(REF_DIR / f"{tag}.json") as f: + return json.load(f) + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_coag_matches_fortran(tag, topo) -> None: + d = _load(tag) + for i, c in enumerate(d["cases"]): + t, p, _inum, _pcore, _scale = c["case"] + got = np.asarray(modal_aero_coag_cam( + jnp.asarray(c["q_in"]), jnp.asarray(t), jnp.asarray(p), + d["deltat"], jnp.asarray(c["dgncur_a"]), + jnp.asarray(c["dgncur_awet"]), jnp.asarray(c["wetdens"]), + topology=topo)) + ref = np.asarray(c["q_out"]) + atol = 1e-13 * np.abs(np.asarray(c["q_in"])) + err = np.abs(got - ref) + bad = np.where(err > atol + 5e-13 * np.abs(ref))[0] + assert bad.size == 0, ( + f"{tag} case {i} diverged at slots {bad.tolist()}: " + f"got {got[bad]}, ref {ref[bad]}") + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_coag_conserves_mass_and_only_loses_number(tag, topo) -> None: + """Coagulation conserves every species' total mass across modes, + strictly loses aitken number, and leaves gases untouched. Also: + coarse (and coarse_strat) modes are in NO pair — their slots must + come back bit-identical.""" + d = _load(tag) + p = CAM_PARAMS[topo.name] + off = p["loffset"] + names = p["cnst_names"] + prefixes = ("so4", "pom", "soa", "bc", "dst", "ncl") + untouched_modes = [m for m in range(topo.nmodes) + if topo.mode_names[m] not in + ("accum", "aitken", "primary_carbon")] + for i, c in enumerate(d["cases"]): + t, pp, _, _, _ = c["case"] + got = np.asarray(modal_aero_coag_cam( + jnp.asarray(c["q_in"]), jnp.asarray(t), jnp.asarray(pp), + d["deltat"], jnp.asarray(c["dgncur_a"]), + jnp.asarray(c["dgncur_awet"]), jnp.asarray(c["wetdens"]), + topology=topo)) + qin = np.asarray(c["q_in"]) + for pre in prefixes: + slots = [j for j, n in enumerate(names) + if n.rsplit("_", 1)[0] == pre and "_a" in n] + if slots: + np.testing.assert_allclose( + got[slots].sum(), qin[slots].sum(), rtol=1e-13, + err_msg=f"{tag} case {i}: {pre} mass not conserved") + n_ait = topo.numptr_amode[topo.mode_index("aitken")] - off + assert got[n_ait] <= qin[n_ait] + assert got[names.index("H2SO4")] == qin[names.index("H2SO4")] + for m in untouched_modes: + slots = [topo.numptr_amode[m] - off] + [ + topo.lmassptr_amode[m][s] - off + for s in range(topo.nspec_amode[m])] + np.testing.assert_array_equal( + got[slots], qin[slots], + err_msg=f"{tag} case {i}: mode {topo.mode_names[m]} " + f"touched by coag") diff --git a/tests/test_cam_driver.py b/tests/test_cam_driver.py new file mode 100644 index 0000000..1b94b8f --- /dev/null +++ b/tests/test_cam_driver.py @@ -0,0 +1,170 @@ +"""End-to-end CAM driver vs the Fortran box model — plan 025 G4b/G5. + +Reference: ``tests/reference/cam_box/*.out`` — four 120-step trajectories +from the ``mam-box-fortran`` **fixdumfac** builds (see the README there): +{cam_mam4, cam_mam5} × {tropospheric, stratospheric}, all-default +namelist. This is the first time MAM5 physics runs against an independent +reference. + +Bars: the reference prints tracers at SEVEN significant digits +(``es14.6``), so per-tracer parity bottoms out at ~5e-7 relative — gated +at 2e-6. The one full-precision column, total sulfur ``totS_mol`` +(``es24.16``), is the machine-precision handle: measured 4.5e-15 on all +four runs, gated at 1e-13. + +Reference-parity settings (and where the defaults deviate): + +* ``n_substeps = 1`` is passed EXPLICITLY by the parity tests — the + reference box is CAM-faithful (no sub-stepping). The package default + is 16 (ADR-021): the A6 measurement (this file's convergence test, + and plan 025 §7) shows first-order splitting error, ~26-78% from + converged at dt=30 s at n=1, halving per doubling. +* ``reseed_dgnwet_each_step = True`` — the box time-manager shim's + ``is_first_step()`` is true EVERY step, so the reference recomputes + sulfeq from fresh post-calcsize dry diameters each step; production + CAM's lagged behaviour is ``False``. +""" +from __future__ import annotations + +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_params import CAM_PARAMS +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +import mam4_jax.coupling.cam_driver as cd +from mam4_jax.physics.cam_saturation import qsat_cam + +REF_DIR = Path(__file__).resolve().parent / "reference" / "cam_box" + +NL = dict(temp=273.0, press=1.0e5, rh=0.9, dt=30.0, nstep=120, + numc=[1.0e8, 1.0e9, 1.0e5, 1.0e0], numc5=1.0e4, + so4frac=[1.0, 1.0, 1.0, 0.0], qso2=1.0e-7, qh2so4=1.0e-11) + + +def build_ic(topo): + """The box driver's initial state (mam_box_driver_cam.F90:279-345): + number from the namelist, so4 mass CONSISTENT with each mode's + prescribed size (calcsize silently rescales inconsistent pairs), + gases vmr→mmr, qv from RH via the table qsat.""" + tb = cd._cam_tables(topo) + p = CAM_PARAMS[topo.name] + rho = NL["press"] / (cd._RAIR * NL["temp"]) + q = np.zeros(p["gas_pcnst"]) + for m in range(topo.nmodes): + numkg = (NL["numc"][m] if m < 4 else NL["numc5"]) / rho + q[tb.num_ptr[m]] = numkg + dg, sg = topo.dgnum_amode[m], topo.sigmag_amode[m] + tmpvol = numkg * (np.pi / 6.0) * dg ** 3 * np.exp(4.5 * np.log(sg) ** 2) + if tb.lptr_so4[m] >= 0: + frac = 1.0 if m == 4 else NL["so4frac"][m] + dens = topo.specdens_amode[topo.specname_amode.index("so4")] + q[tb.lptr_so4[m]] = frac * tmpvol * dens + names = p["cnst_names"] + q[names.index("H2SO4")] = (NL["qh2so4"] + * p["adv_mass"][names.index("H2SO4")] + / p["mwdry"]) + q[names.index("SO2")] = (NL["qso2"] + * p["adv_mass"][names.index("SO2")] + / p["mwdry"]) + _es, qs = qsat_cam(jnp.asarray(NL["temp"]), jnp.asarray(NL["press"])) + nm = topo.nmodes + return { + "q": jnp.asarray(q), "qv": jnp.asarray(NL["rh"] * float(qs)), + "t": jnp.asarray(NL["temp"]), "pmid": jnp.asarray(NL["press"]), + "zm": jnp.asarray(500.0), "pblh": jnp.asarray(1000.0), + "dgncur_a": jnp.zeros(nm), "dgncur_awet": jnp.zeros(nm), + "wetdens": jnp.zeros(nm), "deltat": jnp.asarray(NL["dt"]), + } + + +def load_ref(tag): + rows = [] + with open(REF_DIR / f"{tag}.out") as f: + for line in f: + if not line.startswith("#"): + rows.append([float(x) for x in line.split()[1:]]) + return np.asarray(rows) + + +CASES = [("mam4_nostrat", CAM_MAM4, False), ("mam4_strat", CAM_MAM4, True), + ("mam5_nostrat", CAM_MAM5, False), ("mam5_strat", CAM_MAM5, True)] + + +@pytest.mark.parametrize("tag,topo,strat", CASES) +def test_box_trajectory_matches_fortran(tag, topo, strat) -> None: + tb = cd._cam_tables(topo) + names = CAM_PARAMS[topo.name]["cnst_names"] + adv = np.asarray(tb.adv_mass) + ref = load_ref(tag) + # n_substeps=1: parity with the (un-substepped) reference. The + # package DEFAULT is 16 per ADR-021 — accuracy over reference-parity. + _, traj = cd.cam_run_timesteps(build_ic(topo), NL["nstep"], + topology=topo, strat=strat, + n_substeps=1) + q = np.asarray(traj["q"]) + cols = [ + ("num_a1", q[:, tb.num_ptr[0]]), ("num_a2", q[:, tb.num_ptr[1]]), + ("num_a3", q[:, tb.num_ptr[2]]), + ("so4_a1", q[:, tb.lptr_so4[0]]), ("so4_a2", q[:, tb.lptr_so4[1]]), + ("so4_a3", q[:, tb.lptr_so4[2]]), + ("h2so4", q[:, names.index("H2SO4")]), + ("dgn_a1", np.asarray(traj["dgncur_a"])[:, 0]), + ("dgnwet_a1", np.asarray(traj["dgncur_awet"])[:, 0]), + ("wetdens_a1", np.asarray(traj["wetdens"])[:, 0]), + ("so2", q[:, names.index("SO2")]), + ] + for j, (name, mine) in enumerate(cols): + np.testing.assert_allclose( + mine, ref[:, j], rtol=2e-6, atol=0.0, + err_msg=f"{tag}: {name} left the reference's 7-digit print " + f"floor (~5e-7)") + if topo.nmodes >= 5: + np.testing.assert_allclose(q[:, tb.num_ptr[4]], ref[:, 12], rtol=2e-6) + np.testing.assert_allclose(q[:, tb.lptr_so4[4]], ref[:, 13], rtol=2e-6) + + # Full-precision handle: total sulfur, machine epsilon over 120 steps. + s_slots = [j for j, n in enumerate(names) + if n in ("H2SO4", "SO2") or n.rsplit("_", 1)[0] == "so4"] + totS = (q[:, s_slots] / adv[s_slots]).sum(axis=1) + np.testing.assert_allclose( + totS, ref[:, 11], rtol=1e-13, + err_msg=f"{tag}: full-precision total sulfur diverged") + + +def test_substepping_moves_toward_convergence() -> None: + """A6: the splitting error is first-order — more substeps must move + the answer monotonically toward the converged limit (measured at + dt=30 s: ~60% from converged at n=1 on accum number, halving per + doubling). 20 steps and n ∈ {1, 2, 4} keep this cheap while pinning + both the direction and the rough factor-two reduction.""" + topo = CAM_MAM4 + tb = cd._cam_tables(topo) + finals = {} + for n in (1, 2, 4, 8): + st, _ = cd.cam_run_timesteps(build_ic(topo), 20, topology=topo, + strat=False, n_substeps=n) + finals[n] = float(st["q"][tb.num_ptr[0]]) + err = {n: abs(finals[n] - finals[8]) for n in (1, 2, 4)} + assert err[1] > err[2] > err[4] > 0.0 + assert err[2] < 0.75 * err[1] and err[4] < 0.75 * err[2] + + +def test_documented_defaults() -> None: + """Two load-bearing defaults, each documented: + + * ``n_substeps = 16`` — ADR-021, the owner-decided DEVIATION from + the defaults-reproduce-the-reference convention: CAM's own + splitting is 26-78% from converged at dt=30 s, and shipping that + as the default answer was judged worse than deviating from the + reference. Parity tests opt back into 1 explicitly. + * ``reseed_dgnwet_each_step = True`` — the box reference's + behaviour (its is_first_step() is true every step); False is + production CAM's genuinely lagged wet diameter.""" + import inspect + sig = inspect.signature(cd.cam_run_step) + assert sig.parameters["n_substeps"].default == 16 + assert sig.parameters["reseed_dgnwet_each_step"].default is True diff --git a/tests/test_cam_gasaerexch.py b/tests/test_cam_gasaerexch.py new file mode 100644 index 0000000..4c388a2 --- /dev/null +++ b/tests/test_cam_gasaerexch.py @@ -0,0 +1,122 @@ +"""Validate the CAM gasaerexch port (coupling/cam_driver.py) — plan 025 G1. + +Reference: ``tests/reference/cam_gasaerexch/{mam4,mam5}.json``, captured by +``mam-box-fortran/tools/capture_gasaerexch`` calling the REAL +``modal_aero_gasaerexch_sub`` (cam6_4_187) with prescribed diameters — no +calcsize/wateruptake in the loop, so this isolates exactly what the port +implements: uptake rates → condensation (irreversible tropospheric AND +reversible sulfeq-limited) → the legacy 8-monolayer pcarbon aging → rename +A1 → tendency application. + +The 24-case grid per topology crosses: sulfeq kind (trop / condensing strat +/ evaporating strat) × aitken diameter scale (rename off / firing) × +pcarbon core (saturated aging / fractional aging) × H2SO4 amount. Because +the capture runs the FULL Fortran subroutine — soaexch and nh4 handling +included — parity here also confirms assumption A13 (zero SOA gas + zero +SOA aerosol is a fixed point of soaexch), not just the SO4 arithmetic. +""" +from __future__ import annotations + +import json +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +from mam4_jax.coupling.cam_driver import ( + gas_aer_uptkrates_cam, + modal_aero_gasaerexch_cam, +) + +REF_DIR = Path(__file__).resolve().parent / "reference" / "cam_gasaerexch" + + +def _load(tag): + with open(REF_DIR / f"{tag}.json") as f: + return json.load(f) + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_gasaerexch_matches_fortran(tag, topo) -> None: + """Every case, every tracer: rtol 5e-13, with a PER-SLOT atol of + 1e-13 x that tracer's own initial magnitude. + + The per-slot atol is not tolerance inflation — it defines what is + comparable at all. The post-aging pcarbon number is a pure + cancellation sliver, ``q*(1 - xferfrac_max) ~ q*10eps``: the + reference binary (gfortran -O2 on arm64, -ffp-contract=fast) + FMA-contracts ``q + dqdt*deltat`` into a single rounding, and on a + 10eps sliver that final-ulp difference is ~0.5% RELATIVE while being + ~1e-15 of the tracer itself. Verified exactly: reproducing the + two-rounding chain gives the JAX value bit-for-bit, and the + correctly-rounded FMA gives the Fortran value bit-for-bit. Every + quantity that is not a cancellation remnant of its own input passes + the plain 5e-13 relative bar (atol 0 for slots that start at 0 — + transfer DESTINATIONS are compared strictly). + """ + d = _load(tag) + assert d["nmodes"] == topo.nmodes + deltat = d["deltat"] + for i, c in enumerate(d["cases"]): + t, pmid, kind, _scale, _pcore, _qgas = c["case"] + sulfeq = (None if kind == 0 + else jnp.asarray(c["sulfeq"])) + q_out = modal_aero_gasaerexch_cam( + jnp.asarray(c["q_in"]), jnp.asarray(t), jnp.asarray(pmid), + deltat, jnp.asarray(c["dgncur_a"]), + jnp.asarray(c["dgncur_awet"]), + topology=topo, sulfeq=sulfeq) + ref = np.asarray(c["q_out"]) + got = np.asarray(q_out) + atol = 1e-13 * np.abs(np.asarray(c["q_in"])) + # assert_allclose cannot format an array atol; same criterion by hand. + err = np.abs(got - ref) + bound = atol + 5e-13 * np.abs(ref) + bad = np.where(err > bound)[0] + assert bad.size == 0, ( + f"{tag} case {i} (sulfeq_kind={kind}) diverged at slots " + f"{bad.tolist()}: got {got[bad]}, ref {ref[bad]}") + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_case_grid_genuinely_covers_the_branches(tag, topo) -> None: + """The reference must exercise what it claims: rename firing (aitken + number decreasing), aging firing (pcarbon number decreasing), and + strat evaporation (so4 mass decreasing) each appear somewhere in the + grid — otherwise the parity above proves less than advertised.""" + d = _load(tag) + p = __import__("mam4_jax.core.cam_params", fromlist=["CAM_PARAMS"]) + params = p.CAM_PARAMS[topo.name] + off = params["loffset"] + names = params["cnst_names"] + n_ait = topo.numptr_amode[topo.mode_index("aitken")] - off + n_pca = topo.numptr_amode[topo.mode_index("primary_carbon")] - off + i_so4a1 = names.index("so4_a1") + rename_fired = aging_fired = evaporated = False + for c in d["cases"]: + dq = np.asarray(c["q_out"]) - np.asarray(c["q_in"]) + if dq[n_ait] < 0: + rename_fired = True + if dq[n_pca] < 0: + aging_fired = True + if c["case"][2] == 2 and dq[i_so4a1] < 0: + evaporated = True + assert rename_fired, "no case fired rename" + assert aging_fired, "no case fired pcarbon aging" + assert evaporated, "no strat case evaporated so4" + + +def test_uptkrates_positive_and_size_ordered() -> None: + """Sanity on the third-variant uptake rates: positive, and at equal + number a larger mode takes up more gas (rate grows with diameter in + the continuum-corrected kernel).""" + qnum = jnp.full((4,), 1.0e9 * 28.966) + dg = jnp.asarray([1.1e-7, 2.6e-8, 2.0e-6, 5.0e-8]) * 1.2 + up = gas_aer_uptkrates_cam(qnum, 273.0, 1.0e5, dg, + CAM_MAM4.sigmag_amode) + up = np.asarray(up) + assert np.all(up > 0) + assert up[2] > up[0] > up[3] > up[1] diff --git a/tests/test_cam_microphys.py b/tests/test_cam_microphys.py new file mode 100644 index 0000000..380aee4 --- /dev/null +++ b/tests/test_cam_microphys.py @@ -0,0 +1,103 @@ +"""Validate the CAM microphysics SEQUENCE (mam_microphysics_cam) — plan 025 G4a. + +Reference: ``tests/reference/cam_microphys/{mam4,mam5}.json`` from +``mam-box-fortran/tools/capture_microphys`` — the sibling repo's own +``mam_coupling_cam`` (its transcription of ``aero_model.F90:1202-1247``), +chaining the real gasaerexch → newnuc → coag with the +``del_h2so4_aeruptk`` positive-down bookkeeping across the gasaerexch +call. The components are pinned individually by the G1-G3 tests; this +pins the CHAIN. + +Bar: rtol 5e-12 with the per-slot sliver rule of the G1/G3 tests +(remnants below 1e-10 of the slot's own input carry a 1e-13·q_in atol). +Measured worst: 1.5e-12 — the G1-G3 ulp-level form differences compounded +through three chained stages. +""" +from __future__ import annotations + +import json +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_params import CAM_PARAMS +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +from mam4_jax.coupling.cam_driver import mam_microphysics_cam + +REF_DIR = Path(__file__).resolve().parent / "reference" / "cam_microphys" + + +def _load(tag): + with open(REF_DIR / f"{tag}.json") as f: + return json.load(f) + + +def _run_case(c, deltat, topo): + t, p, qv, zm, pblh, kind, _qg, prod = c["case"] + sulfeq = None if kind == 0 else jnp.asarray(c["sulfeq"]) + return np.asarray(mam_microphysics_cam( + jnp.asarray(c["q_in"]), jnp.asarray(t), jnp.asarray(p), deltat, + jnp.asarray(qv), jnp.asarray(zm), jnp.asarray(pblh), + jnp.asarray(c["dgncur_a"]), jnp.asarray(c["dgncur_awet"]), + jnp.asarray(c["wetdens"]), jnp.asarray(prod), + topology=topo, sulfeq=sulfeq)) + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_sequence_matches_fortran(tag, topo) -> None: + d = _load(tag) + for i, c in enumerate(d["cases"]): + got = _run_case(c, d["deltat"], topo) + ref = np.asarray(c["q_out"]) + atol = 1e-13 * np.abs(np.asarray(c["q_in"])) + bad = np.where(np.abs(got - ref) > atol + 5e-12 * np.abs(ref))[0] + assert bad.size == 0, ( + f"{tag} case {i} diverged at slots {bad.tolist()}: " + f"got {got[bad]}, ref {ref[bad]}") + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_sequence_conserves_sulfur(tag, topo) -> None: + """Gas + all so4 modes is conserved by the whole chain to machine + precision, case by case (condensation, nucleation, coagulation and + both aging paths only MOVE sulfur; production enters q before this + call in the driver design).""" + d = _load(tag) + names = CAM_PARAMS[topo.name]["cnst_names"] + s_slots = [j for j, n in enumerate(names) + if n == "H2SO4" or n.rsplit("_", 1)[0] == "so4"] + for i, c in enumerate(d["cases"]): + got = _run_case(c, d["deltat"], topo) + np.testing.assert_allclose( + got[s_slots].sum(), np.asarray(c["q_in"])[s_slots].sum(), + rtol=1e-13, + err_msg=f"{tag} case {i}: sulfur not conserved by the chain") + + +def test_aeruptk_bookkeeping_feeds_newnuc() -> None: + """The chain must hand newnuc the H2SO4 consumed by condensation: + with strong condensation (trop, high gas) the chained result differs + from running newnuc with aeruptk = 0 on the post-gasaerexch state — + i.e. the bookkeeping is live, not decorative.""" + from mam4_jax.coupling.cam_driver import ( + modal_aero_gasaerexch_cam, modal_aero_newnuc_cam) + d = _load("mam4") + c = next(cc for cc in d["cases"] + if cc["case"][5] == 0 and cc["case"][6] > 1e-10) + t, p, qv, zm, pblh, _k, _qg, prod = c["case"] + args = (jnp.asarray(t), jnp.asarray(p), d["deltat"]) + q0 = jnp.asarray(c["q_in"]) + chained = _run_case(c, d["deltat"], CAM_MAM4) + # newnuc with the bookkeeping zeroed: + q1 = modal_aero_gasaerexch_cam( + q0, *args, jnp.asarray(c["dgncur_a"]), + jnp.asarray(c["dgncur_awet"]), topology=CAM_MAM4, sulfeq=None) + q2 = modal_aero_newnuc_cam( + q1, *args, jnp.asarray(qv), jnp.asarray(zm), jnp.asarray(pblh), + jnp.asarray(prod), jnp.asarray(0.0), topology=CAM_MAM4) + assert not np.allclose(np.asarray(q2), chained, rtol=1e-6), ( + "zeroing del_h2so4_aeruptk changed nothing — the bookkeeping " + "is not being exercised by this state") diff --git a/tests/test_cam_newnuc.py b/tests/test_cam_newnuc.py new file mode 100644 index 0000000..a3aea78 --- /dev/null +++ b/tests/test_cam_newnuc.py @@ -0,0 +1,85 @@ +"""Validate the CAM newnuc wrapper (coupling/cam_driver.py) — plan 025 G2. + +Reference: ``tests/reference/cam_newnuc/{mam4,mam5}.json`` from +``mam-box-fortran/tools/capture_newnuc`` — the REAL ``modal_aero_newnuc_sub`` +(cam6_4_187) over 96 cases per topology crossing warm/cold (the table +qsat's ice branch), in-PBL vs free troposphere (Wang 2008 first-order PBL +adjustment on/off), H2SO4 from just-above-cutoff to strongly nucleating, +production and prior-uptake on/off, and two humidities. + +Bar: rtol 1e-10. The leaf parameterizations are the already-validated +ports (0-diff CAM vs E3SM); what this wrapper adds — the step-average +H2SO4 reconstruction (log/exp chain, ``expm1`` vs the Fortran's +``exp()-1``) and the mixed-phase TABLE qsat — carries ~1-ulp form +differences that the nucleation rate amplifies through its ~10th-power +H2SO4 (and comparable RH) sensitivity: measured worst 2.0e-11 (mam4). +""" +from __future__ import annotations + +import json +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +from mam4_jax.coupling.cam_driver import modal_aero_newnuc_cam +from mam4_jax.physics.cam_saturation import qsat_cam + +REF_DIR = Path(__file__).resolve().parent / "reference" / "cam_newnuc" + + +def _load(tag): + with open(REF_DIR / f"{tag}.json") as f: + return json.load(f) + + +@pytest.mark.parametrize("tag,topo", [("mam4", CAM_MAM4), ("mam5", CAM_MAM5)]) +def test_newnuc_matches_fortran(tag, topo) -> None: + d = _load(tag) + for i, c in enumerate(d["cases"]): + t, p, qv, zm, pblh, _qg, prod, uptk = c["case"] + out = modal_aero_newnuc_cam( + jnp.asarray(c["q_in"]), jnp.asarray(t), jnp.asarray(p), + d["deltat"], jnp.asarray(qv), jnp.asarray(zm), + jnp.asarray(pblh), jnp.asarray(prod), jnp.asarray(uptk), + topology=topo) + np.testing.assert_allclose( + np.asarray(out), np.asarray(c["q_out"]), rtol=1e-10, atol=0.0, + err_msg=f"{tag} case {i} diverged") + + +@pytest.mark.parametrize("tag", ["mam4", "mam5"]) +def test_grid_covers_the_gates(tag) -> None: + """The grid must contain BOTH nucleating and fully-gated cases (the + 4e-16 cutoffs / 100 #/kmol/s floor), or the cutoff logic is untested.""" + d = _load(tag) + fired = sum(1 for c in d["cases"] + if any(o != n for o, n in zip(c["q_out"], c["q_in"]))) + assert 0 < fired < len(d["cases"]), ( + f"{fired}/{len(d['cases'])} fired — gates not exercised") + + +def test_newnuc_conserves_sulfur_exactly() -> None: + """so4_ait gain == H2SO4 loss, case by case (both are mol/mol with + one S each; the wrapper moves mass between exactly these two).""" + d = _load("mam4") + p = __import__("mam4_jax.core.cam_params", fromlist=["CAM_PARAMS"]) + names = p.CAM_PARAMS["cam_mam4"]["cnst_names"] + lg, la = names.index("H2SO4"), names.index("so4_a2") + for c in d["cases"]: + dq = np.asarray(c["q_out"]) - np.asarray(c["q_in"]) + np.testing.assert_allclose(dq[la], -dq[lg], rtol=1e-12, atol=1e-30) + + +def test_table_qsat_differs_from_direct_water_below_freezing() -> None: + """The wrapper must use the mixed-phase TABLE qsat: at 232 K the + ice-blended SVP is materially below the over-water value (that ratio + is why the direct qsat_water would be the wrong reference here).""" + from mam4_jax.physics.strat_sulfate import _qsat_water_cam + t, p = 232.0, 5.0e3 + _es, qs_table = qsat_cam(jnp.asarray(t), jnp.asarray(p)) + qs_water = _qsat_water_cam(jnp.asarray(t), jnp.asarray(p)) + assert float(qs_table) < 0.75 * float(qs_water) diff --git a/tests/test_cam_params.py b/tests/test_cam_params.py new file mode 100644 index 0000000..7590373 --- /dev/null +++ b/tests/test_cam_params.py @@ -0,0 +1,69 @@ +"""Validate the generated CAM parameter layer (core/cam_params.py). + +The values are READ OUT of an initialised CAM box model (sibling repo +`mam-box-fortran`, `tools/dump_tables/to_params.py`) because `specmw_amode` +and `adv_mass` come from the chemistry preprocessor and are not tabulated in +any source file. These tests re-check, from the committed data, the +invariants the generator asserts at generation time — a generator-time +assertion says nothing about what actually landed here — plus the +cross-checks against plan 024 §3's independently-sourced census. +""" +from __future__ import annotations + +import mam4_jax # noqa: F401 +from mam4_jax.core.cam_params import CAM_PARAMS +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 + + +def test_params_align_with_topologies() -> None: + """specmw is per TYPE aligned with Topology.specname_amode; adv_mass + and cnst_names tile the gas window exactly; pcnst = loffset + + gas_pcnst.""" + for topo in (CAM_MAM4, CAM_MAM5): + p = CAM_PARAMS[topo.name] + assert len(p["specmw_amode"]) == len(topo.specname_amode) + assert len(p["adv_mass"]) == p["gas_pcnst"] == len(p["cnst_names"]) + assert topo.pcnst == p["loffset"] + p["gas_pcnst"] + + +def test_tracer_pointers_resolve_to_the_right_names() -> None: + """The topology's lmassptr/numptr indices, shifted into the gas + window, must land on tracers whose NAMES carry the right species + prefix and mode suffix — the strongest committed-data consistency + check available between the two generated files.""" + for topo in (CAM_MAM4, CAM_MAM5): + p = CAM_PARAMS[topo.name] + names, off = p["cnst_names"], p["loffset"] + for m in range(topo.nmodes): + suffix = f"_a{m + 1}" + num_name = names[topo.numptr_amode[m] - off] + assert num_name == "num" + suffix, (topo.name, m, num_name) + for s in range(topo.nspec_amode[m]): + lm = topo.lmassptr_amode[m][s] + t = topo.lspectype_amode[m][s] + spec_name = names[lm - off] + expected = topo.specname_amode[t] + suffix + assert spec_name == expected, (topo.name, m, s, spec_name) + + +def test_specmw_matches_the_plan024_census() -> None: + """Cross-check against the independently-sourced values in plan 024 + §3 (from mam-box-fortran/docs/CESM_VS_E3SM.md): CAM so4 115.107340, + organics/bc 12.011, dust 135.064039, seasalt 58.442468.""" + for topo in (CAM_MAM4, CAM_MAM5): + p = CAM_PARAMS[topo.name] + mw = dict(zip(topo.specname_amode, p["specmw_amode"])) + assert mw["so4"] == 115.10734 + assert mw["pom"] == mw["soa"] == mw["bc"] == 12.011 + assert mw["dst"] == 135.064039 + assert mw["ncl"] == 58.442468 + + +def test_gas_species_present_with_mechanism_mws() -> None: + """The SO4-only driver needs H2SO4 and SO2 by name; their adv_mass + values are the mechanism's (H2SO4 98.0784, SO2 64.0648).""" + for topo in (CAM_MAM4, CAM_MAM5): + p = CAM_PARAMS[topo.name] + names = p["cnst_names"] + assert p["adv_mass"][names.index("H2SO4")] == 98.0784 + assert p["adv_mass"][names.index("SO2")] == 64.0648 diff --git a/tests/test_cam_topology.py b/tests/test_cam_topology.py new file mode 100644 index 0000000..b33538a --- /dev/null +++ b/tests/test_cam_topology.py @@ -0,0 +1,175 @@ +"""The CAM MAM4 and MAM5 topology instances. + +These are the payload of the MAM5 work: `Topology` already accepted `nmodes=5`, +but nothing was registered, so "MAM5-JAX" was a validated shape with no data. + +`mam4_jax/core/cam_topologies.py` is GENERATED in the sibling repo +`mam-box-fortran` by reading the index tables out of an initialised CAM box +model. That indirection is not laziness: `numptr_amode`, `lmassptr_amode` and +the per-slot species properties are not tabulated in any source file -- +`modal_aero_data.F90` builds them at init from the chemistry preprocessor's +species list -- so they cannot be transcribed, only observed. + +The interesting assertion here is the LOSSLESSNESS of `lspectype_amode`. CAM has +no such array; it resolves each (mode, slot) straight to `specdens_amode(l,m)` +and `spechygro(l,m)`. Rather than give `Topology` two shapes, the generator +synthesises a per-type list from species-name prefixes. That is only legitimate +if it round-trips, and the generator asserting it at generation time is not +evidence for the committed data -- so it is re-checked here. +""" +from __future__ import annotations + +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.core import data +from mam4_jax.core.cam_topologies import CAM_MAM4, CAM_MAM5 +from mam4_jax.core.topology import available_topologies, get_topology + +CAM = {"cam_mam4": CAM_MAM4, "cam_mam5": CAM_MAM5} + + +# --- registration ----------------------------------------------------------- + +def test_both_cam_topologies_are_registered() -> None: + for name in CAM: + assert name in available_topologies() + + +def test_importing_them_does_not_change_the_active_topology() -> None: + """Registration must not activate. E3SM stays the default so that importing + the CAM tables cannot silently repoint existing code.""" + assert get_topology() is data.E3SM_MAM4_MOM + + +# --- what MAM5 actually is -------------------------------------------------- + +def test_mam5_has_the_coarse_strat_mode() -> None: + t = CAM_MAM5 + assert t.nmodes == 5 + assert t.variant == "cesm" + assert t.is_mam5 is True + assert t.mode_names[4] == "coarse_strat" + assert t.mode_index("coarse_strat") == 4 + + +def test_coarse_strat_carries_sulfate_only() -> None: + """Mode 5 is the stratospheric sulfate mode: one species, and it is so4.""" + t = CAM_MAM5 + assert t.nspec_amode[4] == 1 + only = t.lspectype_amode[4][0] + assert t.specname_amode[only] == "so4" + assert t.specdens_amode[only] == pytest.approx(1770.0) + assert t.spechygro_amode[only] == pytest.approx(0.507) + + +def test_coarse_strat_size_distribution() -> None: + """Narrower and smaller than the tropospheric coarse mode -- which is why it + takes up sulfate faster in the Fortran (3.4 % vs 0.22 % over an hour).""" + t = CAM_MAM5 + assert t.sigmag_amode[4] == pytest.approx(1.2) + assert t.dgnum_amode[4] == pytest.approx(9e-7) + assert t.dgnumlo_amode[4] == pytest.approx(4e-7) + assert t.dgnumhi_amode[4] == pytest.approx(4e-5) + # Asymmetric about dgnum: 2.25x headroom below, 44.4x above. This is why + # calcsize only ever responds on the low side for mode 5. + assert t.dgnum_amode[4] / t.dgnumlo_amode[4] == pytest.approx(2.25) + assert t.dgnumhi_amode[4] / t.dgnum_amode[4] == pytest.approx(44.44, rel=1e-3) + + +def test_mam4_and_mam5_agree_on_the_first_four_modes_where_they_should() -> None: + """MAM5 is MAM4 plus a mode -- except accum's width, which the strat size + variant changes from 1.8 to 1.6. Asserted rather than assumed, because + 'MAM5 = MAM4 + 1' is the intuition and it is wrong here.""" + assert CAM_MAM4.mode_names == CAM_MAM5.mode_names[:4] + assert CAM_MAM4.nspec_amode == CAM_MAM5.nspec_amode[:4] + assert CAM_MAM4.sigmag_amode[0] == pytest.approx(1.8) + assert CAM_MAM5.sigmag_amode[0] == pytest.approx(1.6) + + +# --- the synthesis must be lossless ---------------------------------------- + +# CAM's own per-(mode, slot) arrays, as read out of the running model. Kept +# here rather than imported so the check compares two independent copies. +CAM_MAM5_SPECDENS_BY_SLOT = ( + (1770.0, 1000.0, 1000.0, 1700.0, 2600.0, 1900.0), + (1770.0, 1000.0, 1900.0, 2600.0), + (2600.0, 1900.0, 1770.0), + (1000.0, 1700.0), + (1770.0,), +) +CAM_MAM5_SPEC_NAMES_BY_SLOT = ( + ("so4_a1", "pom_a1", "soa_a1", "bc_a1", "dst_a1", "ncl_a1"), + ("so4_a2", "soa_a2", "ncl_a2", "dst_a2"), + ("dst_a3", "ncl_a3", "so4_a3"), + ("pom_a4", "bc_a4"), + ("so4_a5",), +) + + +def test_per_type_table_reproduces_cams_per_slot_densities() -> None: + """The round-trip that justifies synthesising lspectype_amode at all.""" + t = CAM_MAM5 + for m, row in enumerate(CAM_MAM5_SPECDENS_BY_SLOT): + for s, expected in enumerate(row): + got = t.specdens_amode[t.lspectype_amode[m][s]] + assert got == pytest.approx(expected), ( + f"mode {m} slot {s}: per-type gives {got}, CAM has {expected}" + ) + + +def test_synthesised_types_match_the_species_names() -> None: + """lspectype_amode[m][s] must point at the type named by the species in + that slot -- otherwise the indices are self-consistent but wrong.""" + t = CAM_MAM5 + for m, row in enumerate(CAM_MAM5_SPEC_NAMES_BY_SLOT): + for s, name in enumerate(row): + prefix = name.rsplit("_", 1)[0] + assert t.specname_amode[t.lspectype_amode[m][s]] == prefix, ( + f"mode {m} slot {s} holds {name} but lspectype points at " + f"{t.specname_amode[t.lspectype_amode[m][s]]}" + ) + + +def test_pom_and_bc_are_distinct_types_despite_both_reading_1e_minus_10() -> None: + """Both hygroscopicities print as 1.0e-10 at low precision but are distinct + float32 round-trips. If the generator had emitted them rounded, the two + types would have collapsed and the synthesis would have been wrong.""" + t = CAM_MAM5 + i_pom = t.specname_amode.index("pom") + i_bc = t.specname_amode.index("bc") + assert t.spechygro_amode[i_pom] != t.spechygro_amode[i_bc] + assert t.specdens_amode[i_pom] != t.specdens_amode[i_bc] + for i in (i_pom, i_bc): + assert t.spechygro_amode[i] == pytest.approx(1e-10, rel=1e-6) + + +# --- derived quantities ----------------------------------------------------- + +@pytest.mark.parametrize("name", sorted(CAM)) +def test_derived_quantities_are_finite_and_ordered(name: str) -> None: + t = CAM[name] + for prop in ("alnsg_amode", "dumfac_amode", "voltonumb_amode", + "voltonumblo_amode", "voltonumbhi_amode"): + arr = np.asarray(getattr(t, prop)) + assert arr.shape == (t.nmodes,) + assert np.isfinite(arr).all(), f"{name}.{prop} not finite: {arr!r}" + # Bigger particles -> fewer per unit volume. + assert (t.voltonumbhi_amode < t.voltonumb_amode).all() + assert (t.voltonumb_amode < t.voltonumblo_amode).all() + + +def test_mam5_dumfac_is_what_the_upstream_bug_reads() -> None: + """The stale-dumfac bug (calcsize) reads the LAST mode's value. Under MAM5 + that is coarse_strat at sigma_g = 1.2, giving +32.5 % on both transfer modes + -- versus +20.6 % on accum alone under MAM4, whose last mode happens to + share aitken's width. This pins the numbers the bug report quotes.""" + import math + stale5 = float(CAM_MAM5.dumfac_amode[-1]) + correct5 = float(CAM_MAM5.dumfac_amode[0]) + assert (correct5 / stale5) ** (1 / 3) == pytest.approx(1.3251, rel=1e-3) + + stale4 = float(CAM_MAM4.dumfac_amode[-1]) + correct4 = float(CAM_MAM4.dumfac_amode[0]) + assert (correct4 / stale4) ** (1 / 3) == pytest.approx(1.2055, rel=1e-3) diff --git a/tests/test_clear_sky_guard.py b/tests/test_clear_sky_guard.py new file mode 100644 index 0000000..4e63bd5 --- /dev/null +++ b/tests/test_clear_sky_guard.py @@ -0,0 +1,104 @@ +"""amicphys must refuse a cloud fraction it cannot represent. + +Only the clear-sky sub-area is ported. With `cldn > 0` the Fortran splits the +cell and area-weights two different sub-area calculations; this port would +instead apply clear-sky physics to the whole cell and return a plausible answer. + +The docstring on `_mam_amicphys_1gridcell` previously *claimed* such a call +"raises a clear error so future workflows don't silently get wrong physics" -- +while the code immediately below declined to check and then never used `cldn` at +all. These tests exist so the claim and the behaviour cannot drift apart again. +""" +from __future__ import annotations + +import warnings + +import jax +import jax.numpy as jnp +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.coupling.amicphys import _check_clear_sky, amicphys + + +def test_zero_cloud_fraction_is_accepted() -> None: + """cldn = 0 is the supported case and must not be blocked.""" + _check_clear_sky(jnp.asarray(0.0)) + _check_clear_sky(0.0) + _check_clear_sky(jnp.zeros(5)) + + +def test_missing_cloud_fraction_is_accepted() -> None: + """Absent means the caller never set it; the box driver defaults to clear.""" + _check_clear_sky(None) + + +@pytest.mark.parametrize("cldn", [0.3, 1.0, 1e-12]) +def test_nonzero_cloud_fraction_is_refused(cldn: float) -> None: + with pytest.raises(NotImplementedError, match="only the clear-sky sub-area"): + _check_clear_sky(jnp.asarray(cldn)) + + +def test_refusal_reports_the_magnitude() -> None: + """The message should say what it saw -- a bare refusal sends the reader + hunting for which field was wrong.""" + with pytest.raises(NotImplementedError, match="3.000e-01"): + _check_clear_sky(jnp.asarray(0.3)) + + +def test_any_nonzero_cell_refuses_not_just_the_mean() -> None: + """A mostly-clear field with one cloudy cell is still unrepresentable.""" + field = jnp.zeros(10).at[7].set(0.5) + with pytest.raises(NotImplementedError): + _check_clear_sky(field) + + +def test_traced_cloud_fraction_returns_silently() -> None: + """Under jit there is no readable magnitude, so nothing can be checked. + + It returns SILENTLY rather than warning. `driver.run_step` is jitted, so the + traced case is the *normal* one -- a warning there would fire on every call, + and a warning that always fires gets filtered, at which point it protects + nothing while still reading as protection. + + The protection for that path lives outside the jit; see + `test_the_driver_guards_before_tracing`. + """ + with warnings.catch_warnings(record=True) as caught: + warnings.simplefilter("always") + jax.jit(_check_clear_sky)(jnp.asarray(0.3)) # must not raise + assert not caught, f"expected silence under trace, got {[str(w.message) for w in caught]}" + + +@pytest.mark.parametrize("entry", ["run_step", "run_timesteps"]) +def test_the_driver_guards_before_tracing(entry: str) -> None: + """This is where the guard has to work. + + `run_step` / `run_timesteps` are jitted, so a check *inside* them can never + fire on a real call. The public names are therefore thin unjitted wrappers + that validate first. Without them the main path had no protection at all -- + only direct `amicphys` calls did. + """ + from mam4_jax import driver + fn = getattr(driver, entry) + args = ({"cldn": jnp.asarray(0.25)},) if entry == "run_step" else ( + {"cldn": jnp.asarray(0.25)}, 2) + with pytest.raises(NotImplementedError, match="clear-sky"): + fn(*args) + + +def test_the_public_names_are_not_themselves_jitted() -> None: + """If these were jitted the guard would be inside the trace again, which is + the bug this arrangement exists to avoid.""" + from mam4_jax import driver + for name in ("run_step", "run_timesteps"): + fn = getattr(driver, name) + assert not hasattr(fn, "_jit_info"), ( + f"driver.{name} is jitted; the cldn guard would be unreachable" + ) + + +def test_the_guard_is_wired_into_the_public_entry() -> None: + """It must run from amicphys(), not only when called directly.""" + with pytest.raises(NotImplementedError, match="clear-sky"): + amicphys({"cldn": jnp.asarray(0.42)}) diff --git a/tests/test_pcarbon_aging.py b/tests/test_pcarbon_aging.py index 53730e4..48fe831 100644 --- a/tests/test_pcarbon_aging.py +++ b/tests/test_pcarbon_aging.py @@ -433,12 +433,15 @@ def test_run_step_params_is_traced_not_static(per_process) -> None: the whole point of params being a traced pytree (a calibration sweep must not recompile per value).""" from mam4_jax.coupling.amicphys import AmicphysParams + from mam4_jax.driver import _run_step_jit # the jitted inner; run_step + # is an unjitted validation wrapper (clear-sky guard), so the cache + # bookkeeping lives one level down. ic = _build_state(per_process["calcsize_before"], step=0) - run_step.clear_cache() + _run_step_jit.clear_cache() out3 = run_step(ic, AmicphysParams(n_so4_monolayers=jnp.asarray(3.0))) - size_after_first = run_step._cache_size() + size_after_first = _run_step_jit._cache_size() out8 = run_step(ic, AmicphysParams(n_so4_monolayers=jnp.asarray(8.0))) - assert run_step._cache_size() == size_after_first, ( + assert _run_step_jit._cache_size() == size_after_first, ( "a new threshold VALUE triggered a recompile — params must be " "traced, not static") # And the values genuinely differ (the sweep measures something). diff --git a/tests/test_rename_cam_branch.py b/tests/test_rename_cam_branch.py new file mode 100644 index 0000000..1ecb342 --- /dev/null +++ b/tests/test_rename_cam_branch.py @@ -0,0 +1,377 @@ +"""CAM's rename algorithm, alongside E3SM's. + +CAM's default path (`modal_aero_rename_no_acc_crs_sub`) and E3SM's production +path (`mam_rename_1subarea` with `rename_method_optaa = 40`) are a real +algorithmic difference — so a CAM driver cannot reuse the existing port. + +The useful discovery is that E3SM's code *contains* CAM's algorithm as its +`optaa /= 40` branch, and CAM's path is line-for-line identical to E3SM's legacy +rename (27 differing lines out of 243, none touching the arithmetic). So this is +one selector, not a second implementation. Three decisions differ +(`mam-box-fortran/docs/reference/discrepancies/rename.md` §4): + +1. whether the growth increment is gated up front, +2. what triggers the old-diameter clamp, +3. whether the old *volume* is rescaled with the clamped diameter. + +WHAT IS AND IS NOT VALIDATED HERE. These tests establish that the CAM branch is +reachable, distinct, conservative, and shows CAM's documented gate behaviour. +They do **not** establish numeric agreement with the Fortran — that needs the +unit and index mapping between CAM's `q`/`dqdt` convention and this module's +amicphys-local view, and a reference set exists for it in `mam-box-fortran` +(`tools/capture_rename`, `outputs/rename_ref/`). That comparison is the next +step and is deliberately not claimed yet. +""" +from __future__ import annotations + +from pathlib import Path + +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 +from mam4_jax.coupling.amicphys import _mam_rename_1subarea + +REF = Path(__file__).resolve().parent / "reference" / "per_process" +AITKEN = 1 # mode order in the amicphys-local view: accum, aitken, coarse, pcarbon +OVERSIZE = 0.01 # scale on aitken number; smaller = fewer, larger particles + + +@pytest.fixture(scope="module") +def local_view(): + b = np.load(REF / "rename_before.npz", allow_pickle=False) + return {k: np.asarray(b[k][0]) for k in + ("qnum_cur", "qaer_cur", "qaer_delsub_grow4rnam", "qwtr_cur", + "fac_m2v_aer")} + + +def _call(v, *, method, num_scale=1.0, growth_scale=1.0): + qn = v["qnum_cur"].copy() + qn[AITKEN] *= num_scale + return _mam_rename_1subarea( + jnp.asarray(qn), + jnp.asarray(v["qaer_cur"]), + jnp.asarray(v["qaer_delsub_grow4rnam"] * growth_scale), + jnp.asarray(v["qwtr_cur"]), + jnp.asarray(v["fac_m2v_aer"]), + method=method, + ) + + +def test_invalid_method_is_rejected(local_view) -> None: + with pytest.raises(ValueError, match="must be 'cam' or 'e3sm'"): + _call(local_view, method="optaa40") + + +def test_default_is_e3sm_so_existing_behaviour_is_unchanged(local_view) -> None: + """The default must stay E3SM: this is a production port and the CAM branch + is new. test_rename.py's Fortran comparison also depends on it.""" + a = _call(local_view, method="e3sm") + b = _mam_rename_1subarea( + jnp.asarray(local_view["qnum_cur"]), + jnp.asarray(local_view["qaer_cur"]), + jnp.asarray(local_view["qaer_delsub_grow4rnam"]), + jnp.asarray(local_view["qwtr_cur"]), + jnp.asarray(local_view["fac_m2v_aer"]), + ) + for x, y in zip(a, b): + assert np.asarray(x).tobytes() == np.asarray(y).tobytes() + + +def test_the_reference_fixture_alone_cannot_tell_the_branches_apart(local_view) -> None: + """Worth pinning: at the captured state the transfer barely engages and the + two algorithms agree exactly. A test suite built only on this fixture would + conclude the CAM branch was a no-op.""" + cam = _call(local_view, method="cam") + e3sm = _call(local_view, method="e3sm") + assert np.allclose(np.asarray(cam[0]), np.asarray(e3sm[0]), rtol=0, atol=0) + + +def test_the_branches_diverge_once_the_mode_is_oversized(local_view) -> None: + """With aitken oversized the old diameter clears `dp_belowcut`, which is + where the clamp and volume-rescale differences bite.""" + cam = _call(local_view, method="cam", num_scale=OVERSIZE) + e3sm = _call(local_view, method="e3sm", num_scale=OVERSIZE) + dn = float(np.max(np.abs(np.asarray(cam[0]) - np.asarray(e3sm[0])))) + assert dn > 0.0, "CAM and E3SM rename must differ in the oversized regime" + + +def test_cam_gates_on_growth_and_e3sm_does_not(local_view) -> None: + """The single most discriminating behaviour. + + CAM gates up front on `dryvol_t_del <= 1e-6 * dryvol_t_oldbnd`, so with no + growth it transfers nothing however oversized the mode is. E3SM skips that + gate (`optaa == 40`) and applies a different one after rescaling. The + Fortran capture shows the same thing: growth 0 gives a zero transfer, and + that was the first thing the capture tool got wrong. + """ + qn_ait = local_view["qnum_cur"][AITKEN] * OVERSIZE + + cam = _call(local_view, method="cam", num_scale=OVERSIZE, growth_scale=0.0) + moved_cam = abs(float(np.asarray(cam[0])[AITKEN]) - qn_ait) + assert moved_cam == 0.0, f"CAM must not transfer without growth; moved {moved_cam:.3e}" + + e3sm = _call(local_view, method="e3sm", num_scale=OVERSIZE, growth_scale=0.0) + moved_e3sm = abs(float(np.asarray(e3sm[0])[AITKEN]) - qn_ait) + assert moved_e3sm > 0.0, ( + "E3SM skips the up-front growth gate, so it should still transfer; if " + "this fails the branches are no longer distinguished by that gate" + ) + + +@pytest.mark.parametrize("method", ["cam", "e3sm"]) +def test_number_and_mass_are_conserved(method: str, local_view) -> None: + """Rename moves material between modes; totals must not change. + + Note the baseline is `qaer_cur` ALONE, not `qaer_cur + qaer_delsub_grow4rnam`. + The growth is already folded into `qaer_cur`; the delta is informational, + used only to form `dryvol_t_del`. Checked against the Fortran reference + itself, which conserves against `qaer_cur` to 0.0 and against + `qaer_cur + delta` to 2.4e-3 — so the wrong baseline reads as a 0.24 % leak. + """ + qn = local_view["qnum_cur"].copy() + qn[AITKEN] *= OVERSIZE + out = _call(local_view, method=method, num_scale=OVERSIZE) + + n0, n1 = qn.sum(), float(np.asarray(out[0]).sum()) + assert abs(n1 - n0) / n0 < 1e-12, f"number not conserved: {n0:.6e} -> {n1:.6e}" + + a0 = local_view["qaer_cur"].sum() + a1 = float(np.asarray(out[1]).sum()) + assert abs(a1 - a0) / a0 < 1e-12, f"aerosol not conserved: {a0:.6e} -> {a1:.6e}" + + +def test_cam_transfer_grows_then_saturates_with_growth(local_view) -> None: + """Signature the Fortran capture showed: the transferred number saturates + (the tail beyond the boundary is finite) while the driver keeps increasing. + A port that scaled without bound would be wrong in a way conservation and + positivity checks cannot see. + """ + qn_ait = local_view["qnum_cur"][AITKEN] * OVERSIZE + moved = [] + for g in (0.0, 0.5, 2.0, 20.0, 200.0): + out = _call(local_view, method="cam", num_scale=OVERSIZE, growth_scale=g) + moved.append(abs(float(np.asarray(out[0])[AITKEN]) - qn_ait)) + + assert moved[0] == 0.0 # gated at zero growth + assert all(b >= a for a, b in zip(moved, moved[1:])), f"not monotone: {moved}" + assert moved[-1] <= qn_ait, "cannot transfer more particles than exist" + # Saturation: the last doubling of growth must move far less than the first. + assert (moved[-1] - moved[-2]) < (moved[2] - moved[1]), f"no saturation: {moved}" + + +# --------------------------------------------------------------------------- +# Numeric validation against CAM's Fortran, done WITHOUT a unit mapping. +# +# The obvious route -- translate CAM's `q`/`dqdt` (mol/mol, #/mol-air) into this +# module's amicphys-local view -- is exactly where a mistake produces a *fake* +# validation: get a factor of 1000 wrong and the comparison either fails for the +# wrong reason or, worse, passes because two errors cancel. +# +# So the comparison is on DIMENSIONLESS quantities instead. Both the inputs and +# the outputs can be made unit-free: +# +# inputs v2n_aitken / voltonumb(accum) = frac (a ratio) +# deldryvol / dryvol = growth (a ratio) +# outputs xferfrac_num = transferred number / initial number +# xferfrac_vol = transferred volume / post-growth volume +# +# The transfer fractions depend only on dgn_t_old, dgn_t_new, dp_cut and the +# mode widths, all of which are fixed by those ratios. So if the algorithm +# matches, the fractions match — with no unit conversion anywhere. +# +# Reference: mam-box-fortran tools/capture_rename, five growth values at +# frac_v2nzz = 0.3, quoted in tests/reference/cam_rename/fractions.json. +# --------------------------------------------------------------------------- + +import json # noqa: E402 + +from mam4_jax.core.data import FAC_M2V_AER, VOLTONUMB_AMODE # noqa: E402 + +CAM_REF = json.loads( + (Path(__file__).resolve().parent / "reference" / "cam_rename" + / "fractions.json").read_text() +) + + +def _transfer_fractions(growth: float, frac_v2nzz: float, dryvol: float): + """Run the CAM branch on a state built from the two dimensionless ratios.""" + fac = np.asarray(FAC_M2V_AER, dtype=np.float64) + n_aer, n_mode = fac.shape[0], 5 + v2n = np.asarray(VOLTONUMB_AMODE, dtype=np.float64) + + qaer = np.zeros((n_aer, n_mode)) + qdel = np.zeros((n_aer, n_mode)) + qnum = np.zeros(n_mode) + for m in range(4): + qaer[0, m] = dryvol / fac[0] + qnum[m] = dryvol * v2n[m] + + # Aitken: oversized, and carrying its post-growth mass with the increment + # recorded separately (qaer_cur is post-growth; the delta is informational). + base = dryvol / fac[0] + qaer[0, AITKEN] = base * (1.0 + growth) + qdel[0, AITKEN] = base * growth + qnum[AITKEN] = dryvol * v2n[0] * frac_v2nzz + + out_num, out_aer, _ = _mam_rename_1subarea( + jnp.asarray(qnum), jnp.asarray(qaer), jnp.asarray(qdel), + jnp.zeros(n_mode), jnp.asarray(fac), method="cam", + ) + n1 = float(np.asarray(out_num)[AITKEN]) + a1 = float(np.asarray(out_aer)[0, AITKEN]) + xf_num = (qnum[AITKEN] - n1) / qnum[AITKEN] + xf_vol = (qaer[0, AITKEN] - a1) / qaer[0, AITKEN] + return xf_num, xf_vol + + +@pytest.mark.parametrize("case", CAM_REF["cases"], + ids=lambda c: f"growth{c['growth']:g}") +def test_cam_branch_matches_the_fortran_transfer_fractions(case) -> None: + """The validation this branch actually rests on. + + Tolerance 1e-8: the Fortran values are quoted to 9 significant figures, so + ~1e-9 is the floor this comparison can resolve. Measured worst case across + the five points is 9.6e-10 — i.e. agreement to the precision of the + reference itself. + """ + xf_num, xf_vol = _transfer_fractions( + case["growth"], CAM_REF["frac_v2nzz"], CAM_REF["dryvol"]) + assert xf_num == pytest.approx(case["xferfrac_num"], rel=1e-8, abs=1e-15) + assert xf_vol == pytest.approx(case["xferfrac_vol"], rel=1e-8, abs=1e-15) + + +def test_both_branches_reproduce_the_fortran_at_these_points() -> None: + """Scope of the comparison above, stated so a passing test is not overread. + + At `frac_v2nzz = 0.3` the two branches agree EXACTLY, so the five-point + match validates the machinery they share -- the erfc tail integrals, + `dp_cut`, `factoraa`/`factoryy`, the transfer-fraction clamps -- and not + CAM's three specific decisions. + + Why they cannot diverge here: `num_t_oldbnd` is clamped into + `[dryvol*v2nhirlx, dryvol*v2nlorlx]`, so `dgn_t_old` saturates regardless of + how far the aitken number is pushed, and both paths end up capped at the + same transfer fraction. Sweeping `frac_v2nzz` from 1.0 down to 0.001 gives + 4.92875520e-01 for both, identically. + + The branches DO differ -- `test_the_branches_diverge_once_the_mode_is_oversized` + and `test_cam_gates_on_growth_and_e3sm_does_not` show that on the captured + reference state. What is missing is a Fortran capture *in a divergent + regime*, which would validate the CAM-specific decisions rather than the + shared code. That is the next step and is recorded in + docs/plans/025-cam-driver.md. + """ + ref = next(c for c in CAM_REF["cases"] if c["growth"] == 2.0) + fac = np.asarray(FAC_M2V_AER, dtype=np.float64) + n_aer, n_mode = fac.shape[0], 5 + v2n = np.asarray(VOLTONUMB_AMODE, dtype=np.float64) + growth, frac, dryvol = 2.0, CAM_REF["frac_v2nzz"], CAM_REF["dryvol"] + + qaer = np.zeros((n_aer, n_mode)); qdel = np.zeros((n_aer, n_mode)) + qnum = np.zeros(n_mode) + for m in range(4): + qaer[0, m] = dryvol / fac[0] + qnum[m] = dryvol * v2n[m] + base = dryvol / fac[0] + qaer[0, AITKEN] = base * (1.0 + growth) + qdel[0, AITKEN] = base * growth + qnum[AITKEN] = dryvol * v2n[0] * frac + + for method in ("cam", "e3sm"): + out = _mam_rename_1subarea( + jnp.asarray(qnum), jnp.asarray(qaer), jnp.asarray(qdel), + jnp.zeros(n_mode), jnp.asarray(fac), method=method) + xf = (qnum[AITKEN] - float(np.asarray(out[0])[AITKEN])) / qnum[AITKEN] + assert xf == pytest.approx(ref["xferfrac_num"], rel=1e-8), ( + f"{method} branch should reproduce the Fortran here; both do" + ) + + +# --------------------------------------------------------------------------- +# The validation that actually pins the CAM branch. +# +# The `fractions.json` comparison above lands in a regime where both branches +# agree, so it validates shared machinery. These points are chosen to sit where +# they DIVERGE, which required working out analytically where that is: +# +# E3SM clamps when dgn_t_old > dp_belowcut (= 0.99*dp_cut) +# CAM clamps when dgn_t_new >= dp_cut +# +# and dgn_t_new = dgn_t_old*(1+growth)^(1/3), so divergence needs an OVERSIZED +# mode with SMALL growth: dgn_t_old just above dp_belowcut while dgn_t_new stays +# below dp_cut, which bounds growth under about 3 %. +# +# Reference: mam-box-fortran tools/capture_rename, parameterised by target +# dgn_t_old. Note that getting there required fixing the capture: rename's +# dryvol_t_old is in m3-AP/kmol-air, i.e. q*(specmw/specdens), NOT raw q. +# Parameterising by raw volume put the intended v2n an order of magnitude below +# the v2nhirlx floor, so num_t_oldbnd clamped every input to the same value and +# the capture returned identical answers for visibly different states. +# --------------------------------------------------------------------------- + +DIVERGENT = json.loads( + (Path(__file__).resolve().parent / "reference" / "cam_rename" + / "divergent.json").read_text() +) + + +def _fractions_at(dgn_old: float, growth: float, method: str): + """Build a state with a given dgn_t_old and growth, return the fractions.""" + from mam4_jax.core.data import ALNSG_AMODE + fac = np.asarray(FAC_M2V_AER, dtype=np.float64) + n_aer, n_mode = fac.shape[0], 5 + v2n = np.asarray(VOLTONUMB_AMODE, dtype=np.float64) + alnsg = np.asarray(ALNSG_AMODE, dtype=np.float64) + factoraa = (np.pi / 6.0) * np.exp(4.5 * alnsg[AITKEN] ** 2) + dryvol = 1.0e-12 + + qaer = np.zeros((n_aer, n_mode)); qdel = np.zeros((n_aer, n_mode)) + qnum = np.zeros(n_mode) + for m in range(4): + qaer[0, m] = dryvol / fac[0] + qnum[m] = dryvol * v2n[m] + base = dryvol / fac[0] + qaer[0, AITKEN] = base * (1.0 + growth) + qdel[0, AITKEN] = base * growth + qnum[AITKEN] = dryvol / (factoraa * dgn_old ** 3) + + out = _mam_rename_1subarea( + jnp.asarray(qnum), jnp.asarray(qaer), jnp.asarray(qdel), + jnp.zeros(n_mode), jnp.asarray(fac), method=method) + n1 = float(np.asarray(out[0])[AITKEN]) + a1 = float(np.asarray(out[1])[0, AITKEN]) + return ((qnum[AITKEN] - n1) / qnum[AITKEN], + (qaer[0, AITKEN] - a1) / qaer[0, AITKEN]) + + +@pytest.mark.parametrize("case", DIVERGENT, + ids=lambda c: f"dgn{c['dgn_old']:.1e}_g{c['growth']:g}") +def test_cam_branch_matches_fortran_where_the_branches_diverge(case) -> None: + """CAM's algorithm, against CAM's Fortran, where it differs from E3SM's. + + Measured worst error across these six points: 8.1e-15 — machine precision, + not a loose tolerance. This is what establishes that CAM's three decisions + are right, as opposed to the machinery they share with E3SM. + """ + xf_num, xf_vol = _fractions_at(case["dgn_old"], case["growth"], "cam") + assert xf_num == pytest.approx(case["xferfrac_num"], rel=1e-12) + assert xf_vol == pytest.approx(case["xferfrac_vol"], rel=1e-12) + + +@pytest.mark.parametrize("case", DIVERGENT, + ids=lambda c: f"dgn{c['dgn_old']:.1e}_g{c['growth']:g}") +def test_the_e3sm_branch_is_wrong_here_so_the_test_discriminates(case) -> None: + """Without this, the test above could pass on a `method="cam"` that silently + fell through to the E3SM path. + + E3SM is off by 68 % to 308 % at these points — the branches are not a + rounding difference. + """ + xf_num, _ = _fractions_at(case["dgn_old"], case["growth"], "e3sm") + rel = abs(xf_num - case["xferfrac_num"]) / abs(case["xferfrac_num"]) + assert rel > 0.5, ( + f"E3SM branch is within {rel:.1%} of CAM here, so this point does not " + "discriminate between the algorithms" + ) diff --git a/tests/test_strat_sulfate.py b/tests/test_strat_sulfate.py new file mode 100644 index 0000000..bfae6bc --- /dev/null +++ b/tests/test_strat_sulfate.py @@ -0,0 +1,239 @@ +"""Validate the CAM sulfeq cluster port (physics/strat_sulfate.py). + +Reference: ``tests/reference/cam_sulfeq/sulfeq.json``, captured from the +CESM3 Fortran (``cam6_4_187``) by ``mam-box-fortran/tools/capture_sulfeq`` +— see that tool's header for the branch-coverage design of the grid +(both T clamps, all three Tabazadeh activity regimes plus both activity +clamps, Kelvin-strong through Kelvin-negligible diameters). + +Three parity layers, so a disagreement is attributable: + +1. ``_qsat_water_cam`` alone (es and qs) — the saturation base. +2. ``calc_h2so4_wtpct`` alone — the Tabazadeh composition. +3. ``calc_h2so4_equilib_mixrat`` — the full equilibrium routine + (qh2so4_equilib, wtpct, sulden). + +Plus property tests the capture cannot express: Kelvin monotonicity in +diameter and reverse-mode gradient finiteness (the cluster must be usable +inside a differentiable driver). +""" +from __future__ import annotations + +import json +from pathlib import Path + +import jax +import jax.numpy as jnp +import numpy as np +import pytest + +import mam4_jax # noqa: F401 - enables jax_enable_x64 by default +from mam4_jax.physics.strat_sulfate import ( + _goffgratch_svp_water, + _qsat_water_cam, + calc_h2so4_equilib_mixrat, + calc_h2so4_wtpct, +) + +REF = Path(__file__).resolve().parent / "reference" / "cam_sulfeq" / "sulfeq.json" + + +@pytest.fixture(scope="module") +def ref(): + with open(REF) as f: + d = json.load(f) + return {k: np.asarray(v) for k, v in d.items() + if k in ("qsat", "wtpct", "cases")} + + +def test_qsat_water_cam_matches_fortran(ref) -> None: + """es and qs at machine precision across the full T x p grid, + including T=135 K (es ~ 7.5e-10 Pa) and T=460 K (es >> p, the + ``qs = 1`` saturated branch that distinguishes CAM's svp_to_qsat + from the E3SM box's).""" + t, p, es_ref, qs_ref = ref["qsat"].T + es = np.asarray(_goffgratch_svp_water(jnp.asarray(t))) + qs = np.asarray(_qsat_water_cam(jnp.asarray(t), jnp.asarray(p))) + # The Fortran caps the RETURNED es at p after computing qs + # (wv_sat_methods.F90:248, "consistent with limiters on qs"); the cap + # never feeds qs or wtpct, so the port keeps es raw and the capture's + # es column is compared capped. + np.testing.assert_allclose(np.minimum(es, p), es_ref, rtol=1e-14, + atol=0.0, err_msg="Goff-Gratch es diverged") + np.testing.assert_allclose(qs, qs_ref, rtol=1e-14, atol=0.0, + err_msg="qsat_water qs diverged") + # The saturated branch is genuinely exercised by the grid. + assert np.any(qs_ref == 1.0), "grid never hit the p<=es branch" + + +def test_wtpct_matches_fortran(ref) -> None: + """Tabazadeh composition at machine precision, all three activity + regimes (the capture grid pins <0.05, 0.05-0.85, >0.85 and both + activity clamps by construction).""" + t, p, qh2o, w_ref = ref["wtpct"].T + w = np.asarray(calc_h2so4_wtpct(jnp.asarray(t), jnp.asarray(p), + jnp.asarray(qh2o))) + np.testing.assert_allclose(w, w_ref, rtol=1e-13, atol=0.0, + err_msg="calc_h2so4_wtpct diverged") + # Both clamps of the output range appear in the reference. + assert w_ref.min() == 25.0 + assert w_ref.max() < 100.0 + + +def test_equilib_mixrat_matches_fortran(ref) -> None: + """The full routine. qeq spans ~46 decades across the grid, so the + bar is relative-only; exp() amplifies its ~100-magnitude exponent's + last ULP by ~1e-14 relative, hence 5e-13 rather than 1e-15.""" + t, p, qh2o, d, qeq_ref, w_ref, sd_ref = ref["cases"].T + qeq, w, sd = calc_h2so4_equilib_mixrat( + jnp.asarray(t), jnp.asarray(p), jnp.asarray(qh2o), jnp.asarray(d)) + np.testing.assert_allclose(np.asarray(qeq), qeq_ref, rtol=5e-13, atol=0.0, + err_msg="qh2so4_equilib diverged") + np.testing.assert_allclose(np.asarray(w), w_ref, rtol=1e-13, atol=0.0, + err_msg="Kelvin-adjusted wtpct diverged") + np.testing.assert_allclose(np.asarray(sd), sd_ref, rtol=1e-13, atol=0.0, + err_msg="sulden diverged") + + +def test_kelvin_raises_equilibrium_for_smaller_particles() -> None: + """akas = exp(+akelvin/r) > 1 and increases as r shrinks, so qeq must + be strictly decreasing in dmean at fixed (T, p, qh2o). (The upstream + comment says 'reduce'; the arithmetic multiplies — this pins the + ported arithmetic, not the comment.)""" + t, p = 210.0, 3.0e3 + qh2o = 0.5 * float(_qsat_water_cam(jnp.asarray(t), jnp.asarray(p))) + d = jnp.asarray([1.0e-8, 1.1e-7, 9.0e-7]) + qeq, _, _ = calc_h2so4_equilib_mixrat(t, p, qh2o, d) + qeq = np.asarray(qeq) + assert qeq[0] > qeq[1] > qeq[2] > 0.0 + + +def test_equilib_grad_finite_across_branches() -> None: + """Reverse-mode gradients stay finite in every activity regime and at + both T clamp edges — the double-where guards on the Tabazadeh + branches and the saturated-qs branch are what this locks in.""" + def qeq_scalar(t, qh2o, d): + out, _, _ = calc_h2so4_equilib_mixrat(t, 3.0e3, qh2o, d) + return out + + grad = jax.grad(qeq_scalar, argnums=(0, 1, 2)) + for t, activ in [(135.0, 0.5), (210.0, 1e-7), (210.0, 0.5), + (210.0, 0.95), (460.0, 0.5)]: + qs = float(_qsat_water_cam(jnp.asarray(min(max(t, 140.0), 450.0)), + jnp.asarray(3.0e3))) + g = grad(jnp.asarray(t), jnp.asarray(activ * qs), jnp.asarray(1.1e-7)) + for name, gi in zip(("t", "qh2o", "dmean"), g): + assert np.isfinite(float(gi)), ( + f"d(qeq)/d({name}) non-finite at T={t}, activ={activ}") + + +# --------------------------------------------------------------------------- +# h2so4_reversible_uptake — the gasaerexch consumer of the cluster +# --------------------------------------------------------------------------- + +def _fortran_reversible_uptake(qgas, qaer_so4, uptk, sulfeq, deltat, ido): + """Verbatim NumPy transcription of modal_aero_gasaerexch.F90:523-566 + (loops, ``1 - exp``, per-mode cycle), as an independent reference. + The JAX port's only arithmetic deviation is ``-expm1(-kxt)``.""" + dtxx = deltat * (1.0 + 1.0e-15) + n_modes = len(ido) + kxt = dtxx * sum(uptk[n] for n in range(n_modes) if ido[n] > 0) + pxt = sum(uptk[n] * sulfeq[n] for n in range(n_modes) if ido[n] > 0) + pxt = max(0.0, pxt * dtxx) + if kxt >= 1.0e-5: + g_equ = pxt / kxt + g_avg = g_equ + (qgas - g_equ) * (1.0 - np.exp(-kxt)) / kxt + else: + g_avg = qgas * (1.0 - 0.5 * kxt) + 0.5 * pxt + dqdt = np.zeros(n_modes) + for n in range(n_modes): + if ido[n] <= 0: + continue + a_bgn = qaer_so4[n] if ido[n] == 1 else 0.0 + a_end = max(0.0, a_bgn + dtxx * uptk[n] * (g_avg - sulfeq[n])) + dqdt[n] = (a_end - a_bgn) / dtxx + return dqdt + + +def test_reversible_uptake_matches_fortran_transcription() -> None: + """Randomized sweep spanning both g_avg branches, condensation and + evaporation, the a_end floor, and all three ido classes. Bar 5e-11: + the expm1-vs-(1-exp) form difference peaks at ~2e-11 relative right + at the kxt = 1e-5 branch threshold (documented deviation).""" + from mam4_jax.physics.strat_sulfate import h2so4_reversible_uptake + rng = np.random.default_rng(20260826) + ido = np.array([1, 1, 2, 1]) # accum/aitken/pcarbon/coarse + for _ in range(300): + deltat = float(rng.uniform(1.0, 1800.0)) + # uptake rates spanning kxt from ~1e-8 to ~1e2 across the sweep + uptk = rng.uniform(0.1, 1.0, 4) * 10.0 ** rng.uniform(-11, -1) + qgas = float(10.0 ** rng.uniform(-16, -9)) + qaer = rng.uniform(0.1, 1.0, 4) * 10.0 ** rng.uniform(-15, -9) + sulfeq = rng.uniform(0.1, 1.0, 4) * 10.0 ** rng.uniform(-18, -8) + ref = _fortran_reversible_uptake(qgas, qaer, uptk, sulfeq, + deltat, ido) + dqdt, total = h2so4_reversible_uptake( + jnp.asarray(qgas), jnp.asarray(qaer), jnp.asarray(uptk), + jnp.asarray(sulfeq), jnp.asarray(deltat), jnp.asarray(ido)) + np.testing.assert_allclose( + np.asarray(dqdt), ref, rtol=5e-11, atol=1e-40, + err_msg="dqdt_so4 diverged from the Fortran transcription") + np.testing.assert_allclose(float(total), ref.sum(), + rtol=5e-11, atol=1e-40) + + +def test_reversible_uptake_equilibrium_is_a_fixed_point() -> None: + """g_bgn == sulfeq_n == s for every active mode: pxt = kxt*s exactly, + so g_avg = s and every tendency is exactly zero — no drift at + equilibrium, to the bit.""" + from mam4_jax.physics.strat_sulfate import h2so4_reversible_uptake + s = 3.7e-12 + dqdt, total = h2so4_reversible_uptake( + jnp.asarray(s), jnp.asarray([1e-11, 2e-12, 0.0, 5e-13]), + jnp.asarray([1e-4, 3e-5, 2e-6, 4e-7]), jnp.full((4,), s), + jnp.asarray(600.0), jnp.asarray([1, 1, 2, 1])) + np.testing.assert_array_equal(np.asarray(dqdt), np.zeros(4)) + assert float(total) == 0.0 + + +def test_reversible_uptake_evaporates_but_never_below_zero() -> None: + """Over-saturated modes (sulfeq > g) evaporate: dqdt < 0 where the + mode holds so4, and the floor stops evaporation at a_end = 0 (a mode + can lose at most a_bgn/dtxx). The slotless ido=2 mode and the + inactive ido=0 mode contribute nothing.""" + from mam4_jax.physics.strat_sulfate import h2so4_reversible_uptake + deltat = 600.0 + dtxx = deltat * (1.0 + 1.0e-15) + qaer = np.array([1e-11, 1e-18, 0.0, 0.0]) + dqdt, _ = h2so4_reversible_uptake( + jnp.asarray(1e-15), jnp.asarray(qaer), + jnp.asarray([1e-3, 1e-3, 1e-3, 1e-3]), + jnp.full((4,), 1e-9), # sulfeq >> gas: evaporation + jnp.asarray(deltat), jnp.asarray([1, 1, 2, 0])) + dqdt = np.asarray(dqdt) + assert dqdt[0] < 0.0 + # mode 1 has almost nothing: the floor limits the loss to a_bgn/dtxx + np.testing.assert_allclose(dqdt[1], -qaer[1] / dtxx, rtol=1e-12) + assert dqdt[2] == 0.0 and dqdt[3] == 0.0 + + +def test_reversible_uptake_branch_continuity_and_grads() -> None: + """The two g_avg forms agree to first order at the kxt = 1e-5 + threshold (relative gap ~kxt²/6 ≈ 2e-11), and reverse-mode gradients + are finite on both sides of every where().""" + from mam4_jax.physics.strat_sulfate import h2so4_reversible_uptake + + def total_at(scale): + _, tot = h2so4_reversible_uptake( + jnp.asarray(2e-12), jnp.asarray([1e-11, 4e-12]), + scale * jnp.asarray([0.6, 0.4]), jnp.asarray([1e-12, 3e-12]), + jnp.asarray(1.0), jnp.asarray([1, 1])) + return tot + + lo = float(total_at(jnp.asarray(0.999e-5))) + hi = float(total_at(jnp.asarray(1.001e-5))) + np.testing.assert_allclose(lo, hi, rtol=1e-2) + + for s in (0.5e-5, 2e-5, 1e-1): + g = jax.grad(lambda x: total_at(x))(jnp.asarray(s)) + assert np.isfinite(float(g)), f"grad non-finite at uptk scale {s}"