diff --git a/.claude/CLAUDE.md b/.claude/CLAUDE.md index 0e29fca..37f3843 100644 --- a/.claude/CLAUDE.md +++ b/.claude/CLAUDE.md @@ -72,7 +72,8 @@ tests/cpp/ plain-C++ suite, no R, no framework tests/cpp/root_network.hpp the suite's root-architecture fixture: the two ex-Leaf-default beta_R_* constants, in ONE place because the golden file's bit-exactness depends on them -tests/cpp/golden/ bit-exact regression baseline, 288 operating points +tests/cpp/golden/ bit-exact regression baseline, 576 operating points + -- one 288-point state grid at 25 and 40 C tests/cpp/bench_solve.cpp timing harness for the collar solve (hazard 5) tests/cpp/bench_gradient.cpp timing harness for a TRAIT GRADIENT: the IFT composite against differencing the solve, with @@ -87,7 +88,10 @@ tests/testthat/gradient_golden.tsv on that platform only, like tests/cpp/golden/ -- these are derivatives of argmax-evaluated outputs, so they inherit its sqrt-amplified class and - disagree cross-platform by up to 1.3e-4 + disagree cross-platform by up to 1.3e-3 -- ten + times the solved outputs, because a finite + difference divides the solver floor by the step + and `R_d_25`'s step is the smallest here tests/validate/ R scripts comparing against plant (needs R) CMakeLists.txt the no-R build: C++ and Python consumers, and the thing that makes "does not need R" runnable @@ -276,12 +280,20 @@ while looking like history. Two rows were produced that way before it was notice ## The golden file is the safety net — treat it that way -`tests/cpp/golden/operating_points.tsv` records 288 operating points and is -compared **bit-exactly** (`%.17g` round-trips a double). It is what makes a large -refactor of this code checkable rather than hopeful, and it earned that role -repeatedly: it proved three "surely dead" `set_physiology` arguments really were -dead, confined the shutdown fix to exactly 48 rows × 5 fields, and showed the -`area_leaf` change was 2 ULP. +`tests/cpp/golden/operating_points.tsv` records 576 operating points — one +288-point state grid at 25 and 40 °C — and is compared **bit-exactly** (`%.17g` +round-trips a double). It is what makes a large refactor of this code checkable +rather than hopeful, and it earned that role repeatedly: it proved three "surely +dead" `set_physiology` arguments really were dead, confined the shutdown fix to +exactly 48 rows × 5 fields, and showed the `area_leaf` change was 2 ULP. + +⚠️ **A grid at one leaf temperature is blind to every temperature response in the +model**, because every reference value is *defined* at 25 °C and a change to any +response curve is inert there **by construction**. Hence the second temperature, and +hence the classification being printed per temperature: points move between branches +as the leaf warms (dry-pinned 18 → 0, wet-pinned 24 → 80). Temperature is the +OUTERMOST loop, which is what lets a regeneration that adds one be checked as an +addition — the 25 °C block must come out byte-identical. **Only run `make golden` deliberately.** Running it after an accidental change rubber-stamps the change. If a diff is intended, regenerate and say so in the @@ -336,33 +348,26 @@ magnitude apart: | field | gcc | clang | why | |---|---|---|---| -| `profit` | **1.82e-07** | **1.82e-07** | it is the maximum itself — well-conditioned | +| `profit` | **2.14e-09** | **2.14e-09** | it is the maximum itself — well-conditioned | | the other eight | **1.4e-04** | **1.4e-04** | evaluated at the **argmax** — sqrt-amplified | -**These figures changed when PLAN 11a replaced the collar solver, and how they -changed is informative.** They were `profit` 1.85e-06 / 5.87e-07 and the other -eight 5.53e-04 / 2.73e-04. Two things to take from the move: - -- **The gcc-versus-clang split was itself a golden-section artefact.** The two - compilers now report *identical* figures, where they used to differ by 2–3×. What - differed between them was which way a golden-section comparison fell; what is - left is libm's `exp`/`pow`, which is a property of the platform and not of the - compiler. So do not expect a compiler-dependent column here any more — and if one - reappears, something has reintroduced a discrete decision into the solve. -- **The sqrt story now fits better than it did.** `sqrt(1.82e-07)` ≈ 4.3e-04 - against the 1.4e-04 observed, where before it was `sqrt(1.85e-06)` ≈ 1.4e-03 - against 5.5e-04. Same order in both cases, but the residual factor shrank, which - is what you would expect once the argmax stopped carrying an extra `GSS_tol_abs` - of arbitrary displacement on top of the flat-maximum amplification. - -The maximum is *flat*: curvature measured directly at the two worst points gives -k ≈ 1.0 and 0.9 in `profit ≈ p* − k(psi_stem−x*)²`. For a flat maximum an error -`dp` in the profit **value** displaces its **location** by `sqrt(dp/k)`, which is -why the well-conditioned column sits three orders below the other. Checked -pointwise — at those points the residuals imply k = 1.01 and 1.70 against the 1.0 -and 0.9 measured from the curvature. It is *not* a global identity: the two column -maxima fall at different operating points, so `sqrt(worst profit)` is not meant to -reproduce `worst argmax`. +Read off CI's summary line: 3757 of 5184 values differ, against tolerances of 1e-05 +and 5e-03. ⚠️ **This table is a CI reading and nothing asserts it, so it goes stale +silently** — it has been wrong three times. Read the summary line, never the FAIL +lines, which are truncated at 20 and biased toward whichever rows come first. + +gcc and clang report *identical* figures. They used to differ by 2–3×, and what +differed was which way a golden-section comparison fell; since PLAN 11a removed that +search, what is left is libm's `exp`/`pow` — a property of the platform, not the +compiler. If a compiler-dependent column reappears, something has reintroduced a +discrete decision into the solve. + +**Why the two classes are five orders apart:** the maximum is *flat*, with curvature +k ≈ 1.0 measured directly at the worst points in `profit ≈ p* − k(psi_stem−x*)²`, so +an error `dp` in the profit **value** displaces its **location** by `sqrt(dp/k)`. +That is a mechanism, not an identity — `sqrt(2.14e-09)` ≈ 4.6e-05 against the 1.4e-04 +observed, because the two column maxima fall at *different* operating points. Do not +expect `sqrt(worst profit)` to predict `worst argmax`. Two things follow that matter beyond this file: diff --git a/.github/workflows/cpp-tests.yml b/.github/workflows/cpp-tests.yml index 01b54f3..7ce47d7 100644 --- a/.github/workflows/cpp-tests.yml +++ b/.github/workflows/cpp-tests.yml @@ -188,9 +188,13 @@ jobs: d.PPFD = 900; d.psi_soil = {2.0}; d.soil_depth = soil_depth; d.atm_vpd = 2.0; d.ca = 40.0; d.leaf_temp = 25.0; d.atm_o2_kpa = 21.0; d.atm_kpa = 101.3; + // ⚠️ ALL n_pars ELEMENTS, WRITTEN OUT: a short initialiser compiles + // and zero-fills the rest, so adding a parameter would silently pass + // 0.0 for it here. The traits in set_traits' order, then the two + // non-traits. double theta[phylloptim::gradient::n_pars] = { 96.0, 2.680147, 3.898245, 5.870283, 2.680147, 3.898245, - 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, + 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, 1.44, 1.0 * 0.000157 / 5.0, 0.0}; const int pars[1] = {0}; // vcmax_25 const std::vector obs{d, d}; @@ -207,7 +211,7 @@ jobs: } // The R layer's arbitrated reference for this operating point, loosely // compared for the same reason profit is below. - if (std::fabs(g[0].grad[0] - 0.0172086) > 1e-5) { + if (std::fabs(g[0].grad[0] - 0.0209349) > 1e-5) { return 1; } l.set_physiology(roots, 900, {2.0}, soil_depth, diff --git a/NEWS.md b/NEWS.md index d508ee6..919a946 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,167 @@ # phylloptim 0.2.1 +## `R_d_25` is a trait, and respiration rises with temperature (#41) + +Dark respiration was `rd_to_vcmax_ratio_ * vcmax_(T)`: a fixed fraction of Vcmax, +unreachable from R, and — because it inherited Vcmax's **peaked** Arrhenius — it +**fell** above the thermal optimum, where real dark respiration rises. No value of +the fraction repairs a function of the wrong shape. + +Now `R_d_25` is a `leaf_traits()` trait like any other, and the response is +Tjoelker's declining Q10: + +``` +Q10(T) = rd_q10_intercept_ - rd_q10_slope_ * (T + 25) / 2 3.09, 0.0430 +R_d(T) = R_d_25 * Q10(T)^((T - 25) / 10) +``` + +The Q10 is evaluated at the mean of T and the reference, which is the form the +land-surface literature implements. Set the slope to zero and the intercept is a +constant Q10, for anyone who wants the conventional form; a constant Q10 of 2 was +tried first and measured too aggressive (R_d 2.8× its 25 °C value over 15 K, −73% on +assimilation at 40 °C, no operating point at all by 45 °C). + +**There is no fallback and no sentinel.** `R_d_25` defaults to **1.44** — which is +`0.015 * 96`, the value the old derivation gave at the default `vcmax_25`, and the +same double — so a caller who does not touch it gets exactly what they got before. +An unset or negative value fails rather than deriving something. + +⚠️ **RESPIRATION NO LONGER FOLLOWS `vcmax_25`.** That is the point of making it a +trait, and it is the one place "same defaults ⇒ same results" has an exception: +a run that *varies* `vcmax_25` used to get proportionally more or less respiration +and now does not. Measured on plant's TF24 SCM, offspring production: + +| | phylloptim master | this branch | +|---|---|---| +| default (`vcmax_25` = 96) | 81.857087216483691 | 81.857087216483691 | +| `vcmax_25` = 60 | 0.40692 | 0.34336 | +| `vcmax_25` = 150 | 73.703 | 92.026 | + +The default arm is bit-identical to all 17 digits. If a study wants respiration to +track Vcmax, that coupling belongs in the caller's parameterisation — plant's +`TF24_hyperpar` is where every other derived parameter is already computed. + +`R_d_25` is also a `pars` entry for `leaf_gradient()` and `leaf_gradient_batch()`: +`dA/dR_d_25 = -0.24874` against a central difference of the solve at −0.24868. ⚠️ Not +≈ −1, because the optimiser moves the operating point in response. `dY/dvcmax_25` is +correspondingly a **partial** at fixed respiration; a fit that moves both adds the +two columns. + +**Blast radius**, and it is zero at 25 °C by construction — the trait *is* the value +there: + +| T | R_d old → new | A old → new | | +|---|---|---|---| +| 15 °C | 0.669 → 0.646 | 6.1505 → 6.1572 | +0.11% | +| 25 °C | 1.440 → 1.440 | 5.5992 → 5.5992 | **exact** | +| 35 °C | 1.610 → 2.592 | 3.4924 → 3.1550 | −9.66% | +| 40 °C | 1.012 → 3.171 | 1.8265 → 0.8555 | −53.16% | +| 45 °C | 0.507 → 3.618 | 0.6339 → −3.6176 | shut-down | + +Two further consequences: + +- **A leaf too hot to gain carbon now shuts down instead of throwing.** A higher R_d + can drive net assimilation negative across the whole `[gamma*, ca]` bracket, and + then `psi_stem_to_ci` has no supply-equals-demand root. The model already knew that + case — `ci_at_compensation_point_` — but only on the energy-balance path; it now + applies on the default path too, and the temperature at which the model stops + having an operating point is pinned as a measurement. +- **On plant's Penman-Monteith path the change is large**, because leaf temperature + there reaches **62 °C, up to +22 K above air**: offspring production −47.2% + (2.2035 → 1.1638). ⚠️ plant's *default* configuration is unaffected — it sets + `leaf_temp` as a constant 25 °C driver with PM off — so the exposure is entirely in + configurations that leave 25 °C. + +`R_d_25` is the fourteenth entry of the gradient enumeration, i.e. in `set_traits()`' +own argument order, with `leaf_specific_conductance_max` and `resistance` after it. +Every index in `gradient.hpp` now has a name (`par_vcmax_25`, `par_R_d_25`, ...) so +nothing indexes `theta` with a bare integer. + +**API removal:** `rd_to_vcmax_ratio_` is gone, from both C++ and the R bindings. It +existed only as the fraction, and there is no fraction now. plant never used it. + +## The golden grid gains a temperature axis: 288 points become 576 (#41) + +⚠️ **A grid at one leaf temperature is blind to every temperature response in the +model**, and this one was, at 25 °C. The reference values of Vcmax, Jmax and R_d are +*defined* there, so a change to any response curve is inert **by construction** — the +respiration change above moved results at every temperature except 25 °C and this +file did not move a bit. + +The grid is now the same 288 operating points at **25 and 40 °C**, with a `leaf_temp` +column. 40 °C is where the response bites hardest, and the extra pinned rows at the +hot end are a feature. + +**Regenerated deliberately, and checkable as an addition**: temperature is the +outermost loop, so the 25 °C block is **byte-identical** to the previous file in all +nine output columns. 288 rows added, none moved. + +The classification is counted per temperature now, because it moves: + +| T | interior | pinned wet | pinned dry | shutdown | +|---|---|---|---|---| +| 25 °C | 198 | 24 | 18 | 48 | +| 40 °C | 160 | 80 | 0 | 48 | + +A single total would let points move between branches and still add up. The direction +is physical: a hot leaf assimilates less and respires more, so it has less to gain +from water and its optimum presses against the **wet** bound instead of the dry one. +The 48 shut-down rows do not move, because there it is hydraulics rather than heat +that forbids transpiration. + +`tests/cpp/bench_solve.cpp` deliberately stays at 288 points at 25 °C: a timing +baseline is only useful against its own history (`tools/cost-baseline.tsv`, +`tools/bench_history.sh`). + +## The recorded gradients have their own tolerance + +`gradient_golden.tsv` used the solved-output baseline's tolerance, and that was +wrong. A value there is a **finite difference**, so cross-platform it carries the +solve's ~1e-9 floor **divided by the step** — one amplification more than the outputs +it is built from. The step is relative, so the smallest-magnitude parameter sets the +tolerance for the whole file: `R_d_25` is 1.44 where `vcmax_25` is 96, a 67× smaller +absolute step, and it disagrees 1.3e-03 on Linux against 1.3e-04 for the other +columns. `gradient_golden_tolerance()` is 5e-03, with the arithmetic. + +## The temperature cache now keys on everything it reads, so R_d is genuinely settable (#41) + +Binding the temperature-response parameters to R made them *writable* but not +*effective*. `set_physiology()`'s temperature block was cached on +`(leaf_temp_, atm_o2_kpa_)` alone, justified by "same inputs → bit-identical +outputs, so reusing is exact" — a statement that was true while those parameters +were unreachable C++ members and **became false the moment they were bound**. The +block's outputs depend on fourteen further inputs the key never mentioned. + +The failure was silent. Setting `rd_to_vcmax_ratio_ <- 0.03` on a solved leaf and +re-supplying the same drivers left `R_d` at **1.44** where a freshly built leaf gave +**2.88**, and assimilation unchanged to every digit. Which is the outcome #41 cared +about: a calibration that cannot move respiration absorbs the mismatch into whatever +it *can* move. + +The cache key now covers every scalar `update_temperature_dependent_params()` reads. +Two consequences beyond the reported bug: + +- **It also covers `vcmax_25` and `jmax_25`**, which closes the third and least + visible part of hazard 10 — a bare `l$vcmax_25 <- x` no longer leaves + `vcmax_`/`jmax_`/`R_d_` describing the old value. ⚠️ `set_traits()` is still the + correct way to change a trait; the vulnerability splines and the solved operating + point need clearing too, and a cache key cannot do that. +- ⚠️ **The existing test passed while the feature was broken**, because it pushed + each change through by calling `update_temperature_dependent_params()` directly — + a route no caller has. `test_temperature_params_invalidate_cache` uses the real + one, and fails four ways without this fix. + +**No behaviour change at the defaults**: the golden file is bit-identical, and the +solve is 2.99 against 3.00 µs/solve interleaved ×3, inside the ±0.01 within-process +noise. + +⚠️ **What this does NOT fix**, recorded because the numbers invite it: `R_d` still +inherits Vcmax's *peaked* Arrhenius and therefore **falls** above the thermal +optimum, where real dark respiration rises. No value of the ratio repairs a function +of the wrong shape — see the note in `update_temperature_dependent_params()`. And +`rd_to_vcmax_ratio` is still not a `leaf_traits()` member, so it cannot yet be +fitted or differentiated; it is set as a field. + ## An out-of-domain transport lookup says which spline, and which caller The stem curve is the only interpolator here built with extrapolation disabled, so diff --git a/PLAN.md b/PLAN.md index 23bb6a4..6cb9f4b 100644 --- a/PLAN.md +++ b/PLAN.md @@ -35,7 +35,7 @@ the user-visible history. | [#34](https://github.com/traitecoevo/phylloptim/issues/34) | 6d | Delete plant's `Leaf` bindings | Unblocked (plant #591 merged, and #33 is done). The hazard-7 payoff, and the only stage that can break plant | | [#38](https://github.com/traitecoevo/phylloptim/issues/38) | 38 | `psi_crit` above the curve's domain fails with an error naming neither | Bounds how far `stem_b` can move in one step; see 11f | | [#40](https://github.com/traitecoevo/phylloptim/issues/40) | 40 | Cross-validate the Medlyn path against `plantecophys` | From #6. Ties to #3, which needs Medlyn first-class | -| [#41](https://github.com/traitecoevo/phylloptim/issues/41) | 41 | `R_d` cannot be set from R: `rd_to_vcmax_ratio_` is unbound | From #6. **74% Rd overstatement** for *Q. ilex* against Sabot's data | +| [#41](https://github.com/traitecoevo/phylloptim/issues/41) | 41 | `R_d_25` is a trait, and respiration rises with temperature | **DONE.** From #6. The scale was the smaller half — the SHAPE was peaked and fell above the thermal optimum. Bit-identical at plant's defaults; −47% offspring production on the PM path | | [#49](https://github.com/traitecoevo/phylloptim/issues/49) | 14 | Is `kmax ~ h^-1` defensible? Koçillari et al. 2021 find no height trend | Split out of item 14, which had it filed nowhere | | [#50](https://github.com/traitecoevo/phylloptim/issues/50) | 8 | `H2O_CO2_stom_diff_ratio` is 1.67, the g1 literature uses 1.6 | **2.2% offset** in every reported `g1_eff` | | [#51](https://github.com/traitecoevo/phylloptim/issues/51) | 10c | `kg_to_mol_h2o` and `kg_per_mol_h2o` are not reciprocals | **0.028%**. The bit-identity baseline it was waiting for now exists | @@ -529,15 +529,55 @@ an established external implementation to check against — and #3 needs it first-class. `plantecophys` also solves the coupled system analytically rather than by root-finding, which is worth considering on its own merits. Found doing #6. -## 41. `R_d` cannot be set from R +## 41. `R_d` — DONE, and the shape mattered more than the scale -`rd_to_vcmax_ratio_` became a settable C++ member in #15, but it is **absent from -`inst/RcppR6_classes.yml`** and is not a constructor argument, so from R a fixed -0.015 is imposed. `R_d_` is bound read/write, but every `set_physiology()` recomputes -it. Sabot's data imply ratios of **0.0046–0.0302** — a factor of 6.5 — and for -*Q. ilex* the model uses 0.914 against the data's 0.525, a **74% Rd overstatement** -and a systematic ~4% species-varying bias in A. ⚠️ Item 10b's claim that this -parameter "is now settable" is true of C++ and false from R. +The original complaint: `rd_to_vcmax_ratio_` was a fixed 0.015 and unreachable from +R, while Sabot's data imply 0.0046–0.0302 across 16 species — for *Q. ilex* the model +used 0.914 against the data's 0.525, a **74% overstatement** and a systematic ~4% +species-varying bias in A. + +⚠️ **The shape was wrong, not just the scale, and no value of the ratio could fix +it.** `R_d` was `ratio * vcmax_(T)`, so it inherited Vcmax's **peaked** Arrhenius and +therefore **fell** above the thermal optimum, where real dark respiration rises — the +opposite direction, and an order of magnitude out by 50 °C. Replaced with Tjoelker's +declining Q10. A constant Q10 = 2 was implemented first and rejected on measurement +(R_d 4.07 at 40 °C, −73% on A, no operating point at all by 45 °C). + +`R_d_25` is now a trait like any other: default **1.44** (`0.015 * 96`, the same +double the old derivation gave), no sentinel, no fallback, and an unset value fails. +`rd_to_vcmax_ratio_` is deleted. + +**Back-compatibility, measured.** plant's TF24 SCM offspring production is +**bit-identical at its defaults** — 81.857087216483691 both sides — because plant's +`vcmax_25` is 96 and it pins `leaf_temp` as a constant 25 °C driver with PM off. +⚠️ Two configurations do move, and both are the point rather than a defect: + +| | master | now | +|---|---|---| +| `vcmax_25` = 60 / 150 (respiration no longer follows Vcmax) | 0.40692 / 73.703 | 0.34336 / 92.026 | +| Penman-Monteith on (Tleaf to 62 °C, +22 K above air) | 2.2035 | 1.1638 | + +A study that wants respiration to track Vcmax should say so in its own +parameterisation — plant's `TF24_hyperpar` is where every other derived parameter is +computed. + +**How that A/B was run**, since `compare_with_plant.R` cannot do it (below) and there +is no harness for it: install phylloptim twice (`origin/master` and the branch) into +separate libraries, then install plant twice from a **clean** source copy each time +with `R_LIBS` pointing at one phylloptim library and the site library — a stale +`src/*.o` would silently give you the other arm — and run the same script under each, +with `leaf_temp` and `vcmax_25` varied. ⚠️ Print and CHECK `find.package()` for both +packages in the script: `R_LIBS` falls back to the site build without a word, which +happened here and produced a plausible file describing the wrong package. + +⚠️ **The golden file was blind to all of this** — 288 points at one temperature, where +every reference value is defined. It now carries a 40 °C block as well. + +**Still open:** `compare_with_plant.R`, against plant's own independent `Leaf`, does +not run — item 64. The obstacle is not the constructor signature its header blames: +against plant at 76df7169 both `Leaf()` and `set_physiology()` work, and what stops it +is `root_collar_psi_` versus `opt_root_psi_` (the #25 rename, which flipped the sign) +on top of results deliberately moved by #15, 11a, 11b, #25, #77 and #84. ## 14. Naming, home, publication @@ -880,8 +920,9 @@ actually need, not to police one you could remove.** Done in #15: five dead entities removed and `set_physiology` taken 14 → 11 arguments, three further dead constants deleted, and **thirteen** temperature-response -parameters made settable. ⚠️ One of those, `rd_to_vcmax_ratio_`, is settable in C++ -but **not bound to R** — that is #41, and this item overstated it. +parameters made settable in C++. ⚠️ One of those, `rd_to_vcmax_ratio_`, was never +bound to R — item 41, which resolved it by deleting the parameter rather than +binding it. Fifteen are bound now. `area_leaf` is out of the supply contract, not merely out of `set_physiology`. Why that was safe is a **homogeneity property** rather than a coincidence: every term in @@ -1336,9 +1377,8 @@ established with `stem_b` first. ⚠️ **And the golden file could not have been the regression guard anyway.** It is compared with a 1e-3 tolerance off macOS/arm64 and the defect was 3.4e-5, so a recurrence would pass on Linux. The guard is a test that compares two orderings **in -the same process**, which is exact everywhere and needs no tolerance — all thirteen -traits as predecessors, four permutations, both routes, both `fast_stem_curve` -settings. +the same process**, which is exact everywhere and needs no tolerance — every trait +as a predecessor, four permutations, both routes, both `fast_stem_curve` settings. ### And what it unblocks diff --git a/R/RcppExports.R b/R/RcppExports.R index 4689549..bffcb1a 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -25,8 +25,8 @@ Leaf__perturb_stem_b <- function(obj_, stem_b) { invisible(.Call('_phylloptim_Leaf__perturb_stem_b', PACKAGE = 'phylloptim', obj_, stem_b)) } -Leaf__set_traits <- function(obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24) { - invisible(.Call('_phylloptim_Leaf__set_traits', PACKAGE = 'phylloptim', obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24)) +Leaf__set_traits <- function(obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25) { + invisible(.Call('_phylloptim_Leaf__set_traits', PACKAGE = 'phylloptim', obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25)) } Leaf__proportion_of_conductivity <- function(obj_, psi) { @@ -453,12 +453,28 @@ Leaf__ko_ha___set <- function(obj_, value) { invisible(.Call('_phylloptim_Leaf__ko_ha___set', PACKAGE = 'phylloptim', obj_, value)) } -Leaf__rd_to_vcmax_ratio___get <- function(obj_) { - .Call('_phylloptim_Leaf__rd_to_vcmax_ratio___get', PACKAGE = 'phylloptim', obj_) +Leaf__R_d_25__get <- function(obj_) { + .Call('_phylloptim_Leaf__R_d_25__get', PACKAGE = 'phylloptim', obj_) } -Leaf__rd_to_vcmax_ratio___set <- function(obj_, value) { - invisible(.Call('_phylloptim_Leaf__rd_to_vcmax_ratio___set', PACKAGE = 'phylloptim', obj_, value)) +Leaf__R_d_25__set <- function(obj_, value) { + invisible(.Call('_phylloptim_Leaf__R_d_25__set', PACKAGE = 'phylloptim', obj_, value)) +} + +Leaf__rd_q10_intercept___get <- function(obj_) { + .Call('_phylloptim_Leaf__rd_q10_intercept___get', PACKAGE = 'phylloptim', obj_) +} + +Leaf__rd_q10_intercept___set <- function(obj_, value) { + invisible(.Call('_phylloptim_Leaf__rd_q10_intercept___set', PACKAGE = 'phylloptim', obj_, value)) +} + +Leaf__rd_q10_slope___get <- function(obj_) { + .Call('_phylloptim_Leaf__rd_q10_slope___get', PACKAGE = 'phylloptim', obj_) +} + +Leaf__rd_q10_slope___set <- function(obj_, value) { + invisible(.Call('_phylloptim_Leaf__rd_q10_slope___set', PACKAGE = 'phylloptim', obj_, value)) } Leaf__PPFD___get <- function(obj_) { @@ -743,13 +759,13 @@ Leaf__g1_eff__get <- function(obj_) { #' The differentiable parameters, in the order C++ indexes them #' -#' The thirteen [leaf_traits()] in `set_traits()`'s argument order, then +#' The fourteen [leaf_traits()] in `set_traits()`'s argument order, then #' `leaf_specific_conductance_max` and `resistance`. Exported so that R's own #' copy of this order can be compared against it in a test: R passes integer #' positions into this enumeration, so appending to it is safe and reordering it #' would silently differentiate the wrong parameter. #' -#' @return A character vector of fifteen names. +#' @return A character vector of sixteen names. #' @seealso [leaf_gradient_batch()] #' @examples #' gradient_par_names() diff --git a/R/RcppR6.R b/R/RcppR6.R index 1cee640..f798ac6 100644 --- a/R/RcppR6.R +++ b/R/RcppR6.R @@ -1,6 +1,6 @@ ## Generated by RcppR6: do not edit by hand ## Version: 0.2.4 -## Hash: c2a88577ccd7eee1ede105545f01253c +## Hash: abbaf8a5425a985fb81802acd9b06f64 ##' @importFrom Rcpp evalCpp ##' @importFrom R6 R6Class @@ -102,8 +102,8 @@ NULL perturb_stem_b = function(stem_b) { Leaf__perturb_stem_b(self, stem_b) }, - set_traits = function(vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24) { - Leaf__set_traits(self, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24) + set_traits = function(vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25) { + Leaf__set_traits(self, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25) }, proportion_of_conductivity = function(psi) { Leaf__proportion_of_conductivity(self, psi) @@ -460,11 +460,25 @@ NULL Leaf__ko_ha___set(self, value) } }, - rd_to_vcmax_ratio_ = function(value) { + R_d_25 = function(value) { if (missing(value)) { - Leaf__rd_to_vcmax_ratio___get(self) + Leaf__R_d_25__get(self) } else { - Leaf__rd_to_vcmax_ratio___set(self, value) + Leaf__R_d_25__set(self, value) + } + }, + rd_q10_intercept_ = function(value) { + if (missing(value)) { + Leaf__rd_q10_intercept___get(self) + } else { + Leaf__rd_q10_intercept___set(self, value) + } + }, + rd_q10_slope_ = function(value) { + if (missing(value)) { + Leaf__rd_q10_slope___get(self) + } else { + Leaf__rd_q10_slope___set(self, value) } }, PPFD_ = function(value) { diff --git a/R/gradient-batch.R b/R/gradient-batch.R index 1d75c52..c5a9c56 100644 --- a/R/gradient-batch.R +++ b/R/gradient-batch.R @@ -326,6 +326,10 @@ leaf_gradient_batch <- function(batch, # observation -- and it reads the two non-traits back out of the resolved drivers # for the same reason that one does: theta has to hold the value the solve will # actually use. +# +# The two non-traits are `leaf_specific_conductance_max` and, on the +# single-potential path only, `resistance`: both are DRIVERS that a calibration +# fits like traits (#44), so the enumeration carries them after the traits. .gradient_theta_matrix <- function(batch, traits) { nr <- batch$theta_nrow par_names <- .gradient_par_names() @@ -333,13 +337,16 @@ leaf_gradient_batch <- function(batch, # By NAME, not by position. `leaf_traits()` is in `set_traits()`'s order and # test-gradient.R asserts it, but this is the one place a silent reordering # would produce plausible numbers for the wrong parameters. - tv <- unlist(traits)[par_names[seq_len(length(par_names) - 2L)]] + trait_names <- par_names[seq_len(length(par_names) - 2L)] + tv <- unlist(traits)[trait_names] if (anyNA(tv)) { - stop("`traits` is missing: ", paste(names(tv)[is.na(tv)], collapse = ", "), - call. = FALSE) + stop("`traits` is missing: ", + paste(trait_names[is.na(tv)], collapse = ", "), call. = FALSE) } m[, seq_along(tv)] <- rep(tv, each = nr) m[, length(par_names) - 1L] <- batch$kmax + # NA on the multi-layer path, where there is no such parameter and C++ never + # reads the column. m[, length(par_names)] <- batch$resistance m } diff --git a/R/gradient.R b/R/gradient.R index 4468711..a3e6580 100644 --- a/R/gradient.R +++ b/R/gradient.R @@ -58,7 +58,7 @@ ##' `R_d_` are derived from the traits inside `set_physiology()`, so they are ##' genuinely unknown until the drivers are re-supplied. ##' -##' The reason it is a function rather than thirteen assignable fields is that +##' The reason it is a function rather than fourteen assignable fields is that ##' `leaf$vcmax_25 <- x` could not be made correct. Three separate pieces of ##' derived state go stale on a bare trait write: the two pre-integrated ##' vulnerability splines, the solved operating point, and -- least visibly -- @@ -90,7 +90,7 @@ set_traits <- function(x, traits) { x$set_traits(traits$vcmax_25, traits$stem_c, traits$stem_b, traits$psi_crit, traits$root_c, traits$root_b, traits$root_psi_crit, traits$beta2, traits$jmax_25, traits$a, traits$curv_fact_elec_trans, - traits$curv_fact_colim, traits$cost_scale_TF24) + traits$curv_fact_colim, traits$cost_scale_TF24, traits$R_d_25) invisible(x) } @@ -202,9 +202,9 @@ set_traits <- function(x, traits) { ##' 57-parameter variant costing the same as its 40-parameter one, because ##' `P_model` is 4 in both. ##' -##' ⚠️ **Always pass `pars`.** It is `P_model`, so the default — all fourteen on +##' ⚠️ **Always pass `pars`.** It is `P_model`, so the default — all fifteen on ##' the multi-layer path — is the most expensive thing you can ask for, and a fit -##' that reads four of them pays for ten it discards. +##' that reads four of them pays for eleven it discards. ##' ##' The intercept is a fresh `Leaf` per call, which there is currently no way to ##' avoid (see phylloptim#52); it is 29% of the exact gradient in the study above. @@ -247,10 +247,14 @@ set_traits <- function(x, traits) { ##' @param control a [leaf_control()] object ##' @param supply how water reaches the root collar: [leaf_supply_multilayer()] ##' (the default) or [leaf_supply_single()] -##' @param pars what to differentiate with respect to. Any of the thirteen +##' @param pars what to differentiate with respect to. Any of the fourteen ##' [leaf_traits()] names, plus `"leaf_specific_conductance_max"` and — on the ##' single-potential path only — `"resistance"`. Defaults to all of them. ##' +##' `dY/dvcmax_25` is a PARTIAL at fixed respiration: `R_d_25` is its own trait, +##' so a fit that wants respiration to follow Vcmax moves both and adds the two +##' columns. +##' ##' `beta_R_H` and `beta_R_V` were here until #33 and are not any more: they ##' parameterise the root-architecture model, which the leaf no longer runs, so ##' this function has no way to reach them. Getting a gradient in either means @@ -387,7 +391,7 @@ leaf_gradient <- function(psi_soil, atm_vpd = atm_vpd, ca = ca, leaf_temp = leaf_temp, atm_o2_kpa = atm_o2_kpa, atm_kpa = atm_kpa) - # The differentiable parameters: the thirteen traits, plus the two that are not + # The differentiable parameters: the fourteen traits, plus the two that are not # traits and that a calibration nonetheless fits (#44). See .gradient_theta. theta <- .gradient_theta(traits, leaf_specific_conductance_max, supply, root_network) @@ -616,7 +620,7 @@ leaf_gradient <- function(psi_soil, # Everything this can differentiate, and its current value, as one named vector. # -# The thirteen traits, plus the two quantities a calibration fits that are NOT +# The fourteen traits, plus the two quantities a calibration fits that are NOT # traits (#44) and that `pars` therefore used to reject: # # * `leaf_specific_conductance_max` -- a DRIVER, set through set_drivers(). It @@ -645,6 +649,7 @@ leaf_gradient <- function(psi_soil, theta } + # Push a parameter vector back onto the leaf, in the one order that is correct. # # ⚠️ ORDER IS LOAD-BEARING and the reason this is a function rather than three @@ -709,7 +714,7 @@ leaf_gradient <- function(psi_soil, } # Positional, straight onto the object, rather than through `set_traits()` and # `set_drivers()`. Those two rebuild a `leaf_traits` object with - # `structure(as.list(...))`, re-extract thirteen fields by name, and re-run the + # `structure(as.list(...))`, re-extract fourteen fields by name, and re-run the # driver validation -- 3.0% + 3.3% + 4.9% of a gradient's self time between them, # for work whose answer cannot change across perturbations. # @@ -719,12 +724,14 @@ leaf_gradient <- function(psi_soil, # the #25 positive-magnitude invariants itself. Do not copy this pattern anywhere # the values are not already known-good. # ⚠️ POSITIONAL, so the count is load-bearing. `set_traits()`'s C++ signature and - # `leaf_traits()` must agree on thirteen; if a trait is ever added, this call is - # the one place that will not fail to compile. test-gradient.R asserts the arity. + # `leaf_traits()` must agree on FOURTEEN, and adding a trait breaks here and + # nowhere else -- at run time, with "argument is missing" raised inside + # the generated binding, which names neither this line nor the count. That is + # how #41 broke; test-gradient.R asserts the arity so the next one is caught. tv <- theta[trait_names] apply_traits(tv[[1L]], tv[[2L]], tv[[3L]], tv[[4L]], tv[[5L]], tv[[6L]], tv[[7L]], tv[[8L]], tv[[9L]], tv[[10L]], tv[[11L]], tv[[12L]], - tv[[13L]]) + tv[[13L]], tv[[14L]]) # `resistance` is a driver, so it goes in with the others rather than through # $set_supply_single(). That removes the second object-resetting call this # function used to make -- and with it the reason the ordering note above had to diff --git a/R/leaf-model.R b/R/leaf-model.R index 610db87..090cc15 100644 --- a/R/leaf-model.R +++ b/R/leaf-model.R @@ -45,7 +45,8 @@ a = 0.30, curv_fact_elec_trans = 0.7, curv_fact_colim = 0.99, - cost_scale_TF24 = 7.5 + cost_scale_TF24 = 7.5, + R_d_25 = 1.44 ) .leaf_control_defaults <- list( @@ -86,6 +87,8 @@ ##' @param curv_fact_colim curvature of the colimited photosynthesis equation ##' @param cost_scale_TF24 cost parameter for the TF24 profit model ##' (umol m^-2 s^-1) +##' @param R_d_25 dark respiration at 25 C (umol m^-2 s^-1). It is the value at +##' 25 C only: respiration rises from there on Tjoelker's declining-Q10 curve. ##' ##' @section Where the two root-resistance constants went: ##' `beta_R_H` and `beta_R_V` were traits here until #33. They parameterise the @@ -115,15 +118,20 @@ leaf_traits <- function(vcmax_25 = 96, a = 0.30, curv_fact_elec_trans = 0.7, curv_fact_colim = 0.99, - cost_scale_TF24 = 7.5) { + cost_scale_TF24 = 7.5, + R_d_25 = 1.44) { out <- list(vcmax_25 = vcmax_25, stem_c = stem_c, stem_b = stem_b, psi_crit = psi_crit, root_c = root_c, root_b = root_b, root_psi_crit = root_psi_crit, beta2 = beta2, jmax_25 = jmax_25, a = a, curv_fact_elec_trans = curv_fact_elec_trans, curv_fact_colim = curv_fact_colim, - cost_scale_TF24 = cost_scale_TF24) + cost_scale_TF24 = cost_scale_TF24, + R_d_25 = R_d_25) .check_scalars(out, "leaf_traits") + if (R_d_25 < 0) { + stop("leaf_traits(): R_d_25 must be non-negative", call. = FALSE) + } structure(out, class = c("leaf_traits", "list")) } @@ -365,6 +373,10 @@ leaf_model <- function(traits = leaf_traits(), control = leaf_control(), ci_niter = control$ci_niter, cost_scale_TF24 = traits$cost_scale_TF24 ) + # ⚠️ AFTER construction, because plant's RcppR6 bindings pin the generated + # constructor by arity so R_d_25 cannot be an argument to it. Without this line + # `leaf_traits(R_d_25 = )` would be accepted and silently ignored. + l$R_d_25 <- traits$R_d_25 l$initialize_integrator(control$integration_rule, control$integration_tol) # After the integrator, because set_supply_single clears the solved state -- # not the integrator tolerance, but relying on that ordering would be a diff --git a/inst/RcppR6_classes.yml b/inst/RcppR6_classes.yml index d68a2de..4af1b02 100644 --- a/inst/RcppR6_classes.yml +++ b/inst/RcppR6_classes.yml @@ -156,9 +156,7 @@ Leaf: # # The eight fields above are DERIVED: set_physiology recomputes them from # leaf temperature on every call, so writing one from R is overwritten by - # the next solve. These thirteen are the parameters that generate them, and - # they were public C++ members with no entry here at all -- so from R the - # shape of the temperature response was fixed and unreachable. + # the next solve. These fifteen are the parameters that generate them. # # ⚠️ That is not a small gap. The defaults imply a thermal optimum near # 31.2 C for Vcmax and 27.9 C for Jmax (Topt = H_d / (d_S - R*log(ha/(H_d - @@ -166,19 +164,15 @@ Leaf: # of the reason to reach for this model -- needs to move them. Jones et al. # (2026) fit 35 C for both. # - # ⚠️ `rd_to_vcmax_ratio_` matters for a different reason. Rd is - # `rd_to_vcmax_ratio_ * vcmax_`, so it inherits Vcmax's PEAKED Arrhenius and - # therefore FALLS above the thermal optimum, where a Q10 respiration rises. - # It is fixed at 0.015 while Sabot's own data imply 0.0046 to 0.0302 across - # species -- a factor of 6.5 -- and for Q. ilex the model uses 0.914 against - # the data's 0.525, a 74% overstatement. + # The temperature cache is keyed on every scalar + # `update_temperature_dependent_params()` reads, so setting any of these and + # re-supplying the drivers recomputes, as a caller would expect (#41). + # `test_temperature_params_invalidate_cache` asserts it through the route a + # caller actually takes. # - # ⚠️ SETTING THESE DOES NOT RECOMPUTE ANYTHING. Like the traits (hazard 10), - # they feed a cache: set_physiology's temperature block is keyed on - # (leaf_temp_, atm_o2_kpa_) and on nothing else, so changing one of these - # and calling set_physiology again takes a cache HIT and silently keeps the - # old response. Call set_traits() -- which ends in setup_clean_leaf() and - # clears the cache -- or construct afresh. + # ⚠️ `set_traits()` is STILL the right way to change a TRAIT (`vcmax_25`, + # `jmax_25`, ...): the vulnerability splines and the solved operating point need + # clearing too, and the cache key does not do that. vcmax_ha_: {type: double, access: field} vcmax_H_d_: {type: double, access: field} vcmax_d_S_: {type: double, access: field} @@ -191,7 +185,15 @@ Leaf: kc_ha_: {type: double, access: field} ko_25_: {type: double, access: field} ko_ha_: {type: double, access: field} - rd_to_vcmax_ratio_: {type: double, access: field} + # Dark respiration at 25 C. Bound as a field as well as being a `set_traits()` + # argument, because plant's own bindings pin the generated constructor by arity + # so `leaf_model()` has to apply it afterwards. + R_d_25: {type: double, access: field} + # The Tjoelker (2001) declining-Q10 coefficients: + # Q10(T) = rd_q10_intercept_ - rd_q10_slope_ * (T + 25) / 2 + # Set the slope to zero and the intercept IS a constant Q10. + rd_q10_intercept_: {type: double, access: field} + rd_q10_slope_: {type: double, access: field} # --- drivers, as last set by set_physiology ------------------------------ PPFD_: {type: double, access: field} @@ -318,7 +320,7 @@ Leaf: args: [stem_b: double] set_traits: return_type: void - args: [vcmax_25: double, stem_c: double, stem_b: double, psi_crit: double, root_c: double, root_b: double, root_psi_crit: double, beta2: double, jmax_25: double, a: double, curv_fact_elec_trans: double, curv_fact_colim: double, cost_scale_TF24: double] + args: [vcmax_25: double, stem_c: double, stem_b: double, psi_crit: double, root_c: double, root_b: double, root_psi_crit: double, beta2: double, jmax_25: double, a: double, curv_fact_elec_trans: double, curv_fact_colim: double, cost_scale_TF24: double, R_d_25: double] # --- transpiration and conductance --------------------------------------- proportion_of_conductivity: diff --git a/inst/include/phylloptim/gradient.hpp b/inst/include/phylloptim/gradient.hpp index 004f557..224d33c 100644 --- a/inst/include/phylloptim/gradient.hpp +++ b/inst/include/phylloptim/gradient.hpp @@ -63,23 +63,35 @@ namespace gradient { // --- the parameter enumeration, which R indexes into -------------------------- // -// The thirteen traits in `Leaf::set_traits`' argument order, then the two +// The fourteen traits in `Leaf::set_traits`' argument order, then the two // quantities a calibration fits that are not traits: the conductance driver and // the single-potential path's series resistance. // -// ⚠️ APPENDING IS SAFE AND REORDERING IS NOT. R names these positions in -// `.gradient_par_names` and passes integer indices, so a swap here silently -// differentiates the wrong parameter. `test-gradient-batch.R` reads the names -// back out of C++ and compares them with R's, so the two cannot drift apart -// without a failure. -inline constexpr int n_traits = 13; -inline constexpr int n_pars = 15; - -// The two indices the code below has to know by name: one takes the fast -// homogeneity path, and the two non-traits take a relative step. +// ⚠️ R INDEXES THESE POSITIONS, so a reordering silently differentiates the wrong +// parameter. `test-gradient-batch.R` reads the names back out of C++ and compares +// them with R's, so the two cannot drift apart without a failure. +inline constexpr int n_traits = 14; +inline constexpr int n_pars = 16; + +// Every index by name, so nothing below indexes `theta` with a bare integer. +// The first `n_traits` are `set_traits`' arguments in its order, which is also +// `leaf_traits()`'; the two non-traits follow and take a relative step. +inline constexpr int par_vcmax_25 = 0; +inline constexpr int par_stem_c = 1; inline constexpr int par_stem_b = 2; -inline constexpr int par_kmax = 13; -inline constexpr int par_resistance = 14; +inline constexpr int par_psi_crit = 3; +inline constexpr int par_root_c = 4; +inline constexpr int par_root_b = 5; +inline constexpr int par_root_psi_crit = 6; +inline constexpr int par_beta2 = 7; +inline constexpr int par_jmax_25 = 8; +inline constexpr int par_a = 9; +inline constexpr int par_curv_fact_elec_trans = 10; +inline constexpr int par_curv_fact_colim = 11; +inline constexpr int par_cost_scale_TF24 = 12; +inline constexpr int par_R_d_25 = 13; +inline constexpr int par_kmax = 14; +inline constexpr int par_resistance = 15; inline const std::vector& par_names() { static const std::vector names{ @@ -87,7 +99,7 @@ inline const std::vector& par_names() { "psi_crit", "root_c", "root_b", "root_psi_crit", "beta2", "jmax_25", "a", "curv_fact_elec_trans", "curv_fact_colim", - "cost_scale_TF24", + "cost_scale_TF24", "R_d_25", "leaf_specific_conductance_max", "resistance"}; return names; @@ -268,9 +280,12 @@ inline void apply(Leaf& l, const double* theta, const Drivers& d, bool single, l.perturb_stem_b(theta[par_stem_b]); return; } - l.set_traits(theta[0], theta[1], theta[2], theta[3], theta[4], theta[5], - theta[6], theta[7], theta[8], theta[9], theta[10], theta[11], - theta[12]); + l.set_traits(theta[par_vcmax_25], theta[par_stem_c], theta[par_stem_b], + theta[par_psi_crit], theta[par_root_c], theta[par_root_b], + theta[par_root_psi_crit], theta[par_beta2], theta[par_jmax_25], + theta[par_a], theta[par_curv_fact_elec_trans], + theta[par_curv_fact_colim], theta[par_cost_scale_TF24], + theta[par_R_d_25]); if (single) { // R's `series_resistance()`: a default-constructed network carrying one // series resistance in `r_R_V_sum`, which is that field's own meaning with diff --git a/inst/include/phylloptim/leaf_model.hpp b/inst/include/phylloptim/leaf_model.hpp index a82cea5..8c7eae0 100644 --- a/inst/include/phylloptim/leaf_model.hpp +++ b/inst/include/phylloptim/leaf_model.hpp @@ -14,6 +14,7 @@ #include #include +#include #include #include #include @@ -334,10 +335,31 @@ class Leaf { double kc_ha_ = phylloptim::kc_ha; double ko_25_ = phylloptim::ko_25; // Rubisco Km for O2, umol mol^-1 double ko_ha_ = phylloptim::ko_ha; - // Dark respiration as a fraction of vcmax. Was the bare literal 0.015 inline in - // update_temperature_dependent_params -- a named, species-variable parameter - // (Collatz/Farquhar) hiding as a magic number. - double rd_to_vcmax_ratio_ = 0.015; + // Dark respiration at the 25 C reference, umol m^-2 s^-1. Many datasets report + // it directly (Sabot et al. give `Rlref` per site), and across their 16 species + // the implied fraction of vcmax_25 spans 0.0046 to 0.0302, so it is a trait in + // its own right rather than a fixed multiple of anything. + // + // The default is 0.015 * 96, the value the old vcmax-derived form gave at the + // default vcmax_25. Initialised here rather than in the constructors' init lists + // because plant's RcppR6 bindings pin the 17-argument constructor by arity, so + // this cannot become an 18th argument without breaking plant's generated glue. + double R_d_25 = 1.44; + // Dark respiration's temperature response, Tjoelker et al. (2001): + // + // R_d(T) = R_d_25 * Q10(T)^((T - 25) / 10) + // Q10(T) = rd_q10_intercept_ - rd_q10_slope_ * (T + 25) / 2 + // + // The Q10 is evaluated at the MEAN of the measurement and reference + // temperatures, which is the form the land-surface literature implements, and it + // DECLINES with temperature: a constant Q10 of 2 is too aggressive at the top of + // the range, putting R_d 2.8x its 25 C value over 15 K and leaving the solve no + // operating point at all by 45 C. + // + // Set the slope to zero and the intercept IS a constant Q10, for anyone who + // wants the conventional form. + double rd_q10_intercept_ = 3.09; + double rd_q10_slope_ = 0.0430; double atm_kpa_; // Conversion from a mixing ratio (umol mol^-1) to a partial pressure (Pa). // DERIVED from atm_kpa_, not a constant: it is 1e-6 * P, so the old @@ -392,8 +414,29 @@ class Leaf { // NOTE: electron_transport_ is deliberately NOT cached here -- it also depends // on the per-call PPFD_ and is recomputed every call. bool photo_temp_cached_ = false; - double photo_temp_cache_leaf_temp_ = 0.0; - double photo_temp_cache_atm_o2_kpa_ = 0.0; + // ⚠️ THE KEY MUST COVER EVERY SCALAR THE BLOCK READS, NOT JUST THE DRIVERS. + // It used to be (leaf_temp_, atm_o2_kpa_) alone, and the argument for that was + // "same inputs -> bit-identical outputs, so reusing is exact". That argument was + // true while the temperature-response parameters were unreachable C++ members + // and became FALSE the moment they were bound to R: `l$rd_q10_slope_ <- 0` + // followed by `set_drivers()` at the same temperature took a cache HIT and + // silently kept the old response, with A unchanged to every digit. + // + // So the key is now every input of update_temperature_dependent_params(). Two + // consequences worth knowing: + // + // * it also covers `vcmax_25` and `jmax_25`, which closes the third and least + // visible half of hazard 10 -- a bare `l$vcmax_25 <- x` write no longer + // leaves `vcmax_`/`jmax_`/`R_d_` describing the old value. `set_traits()` is + // still the right way to change a trait (the vulnerability splines and the + // solved point need clearing too), but the silent-wrong-number failure mode + // is gone. + // * the cost is 17 double comparisons per set_physiology() call, i.e. per + // driver set, NOT per inner solve iteration. Measured: within run-to-run + // noise on bench_solve. + static constexpr int photo_temp_key_size = 19; + std::array photo_temp_cache_key_{}; + std::array photo_temp_key() const; std::vector f_r; // TODO: move into environment? @@ -438,13 +481,14 @@ class Leaf { // check here can see the difference, because both are just positive numbers. void set_physiology(const RootNetwork& root_network, double PPFD, const std::vector& psi_soil, const std::vector& soil_depth, double leaf_specific_conductance_max, double atm_vpd, double ca, double leaf_temp, double atm_o2_kpa, double atm_kpa); - // Replace the thirteen traits on an existing Leaf, leaving the four numerical - // controls alone. Same arguments, same order, as the constructor's trait subset. + // Replace the fourteen traits on an existing Leaf, leaving the four numerical + // controls alone. Same arguments, same order, as the constructor's trait subset, + // plus R_d_25 which the constructor does not take. // - // It was fifteen before #33. `beta_R_H` and `beta_R_V` left with the root - // architecture model, so they are no longer traits of anything here and there is - // no route to d(output)/d(beta_R_*) through this object. A caller who needs one - // differences the NETWORK, which is now an input: root_network_from_carbon is + // `beta_R_H` and `beta_R_V` are NOT traits here since #33: they left with the root + // architecture model, so there is no route to d(output)/d(beta_R_*) through this + // object. A caller who needs one differences the NETWORK, which is now an input: + // root_network_from_carbon is // homogeneous of degree 1 in each constant (r_R_H_min proportional to beta_R_H, // r_R_V to beta_R_V), so the perturbed network is a scaling of the base one and // costs no rebuild -- but the two solves either side of it are still two solves. @@ -483,7 +527,7 @@ class Leaf { double root_c, double root_b, double root_psi_crit, double beta2, double jmax_25, double a, double curv_fact_elec_trans, double curv_fact_colim, - double cost_scale_TF24); + double cost_scale_TF24, double R_d_25); // The #25 boundary: the four potentials that must be positive magnitudes. One // copy, called from both the constructor and set_traits -- the alternative is @@ -967,7 +1011,8 @@ class Leaf { // operating point in this state reads NA sentinels. Unsolved, // Interior profit maximum: dprofit == 0 was solved for, strictly inside the - // feasible collar interval. 198 of the 288 golden grid points. + // feasible collar interval. 198 of the 288 golden grid points at 25 C -- 160 of + // them at 40 C, where the optimum presses against the WET bound instead. Interior, // Constrained optimum pinned at the WET end of the feasible interval, just // inside root_zero_E (the collar at which uptake is exactly zero). profit is @@ -984,7 +1029,8 @@ class Leaf { // Shutdown on water: no collar potential both moves water and stays inside // the stem's and the root's critical potentials. The stem holds at psi_crit, // transpiration is zero, and the leaf pays respiration plus the hydraulic - // cost there. 48 of the 288 golden grid points. The water response is zero; + // cost there. 48 of the 288 golden grid points at every temperature, since it is + // hydraulics rather than heat that forbids transpiration. The water response is zero; // the carbon response is not. HydraulicShutdown, // Shutdown on light: assim_max_ < 0, so gross assimilation at ci = ca cannot @@ -1146,14 +1192,14 @@ inline void Leaf::check_psi_magnitudes(double psi_crit, double stem_b, } } -// See the header for why this exists rather than fifteen settable fields. +// See the header for why this exists rather than fourteen settable fields. inline void Leaf::set_traits(double vcmax_25_, double stem_c_, double stem_b_, double psi_crit_, double root_c_, double root_b_, double root_psi_crit_, double beta2_, double jmax_25_, double a_, double curv_fact_elec_trans_, double curv_fact_colim_, - double cost_scale_TF24_) { + double cost_scale_TF24_, double R_d_25_) { check_psi_magnitudes(psi_crit_, stem_b_, root_b_, root_psi_crit_); // Which splines have to be rebuilt, decided BEFORE the assignment. Exact @@ -1182,6 +1228,7 @@ inline void Leaf::set_traits(double vcmax_25_, double stem_c_, double stem_b_, curv_fact_elec_trans = curv_fact_elec_trans_; curv_fact_colim = curv_fact_colim_; cost_scale_TF24 = cost_scale_TF24_; + R_d_25 = R_d_25_; roots_.root_c = root_c_; roots_.root_b = root_b_; @@ -1364,17 +1411,16 @@ inline void Leaf::set_physiology(const RootNetwork& root_network, double PPFD, c // candidate psi in set_leaf_states_rates_from_psi_stem, so we always recompute // the Tair baseline (used for assim_max_ / feasibility) and let the solve // override it. + const std::array photo_key = photo_temp_key(); if (!use_energy_balance_ && photo_temp_cached_ && - leaf_temp_ == photo_temp_cache_leaf_temp_ && - atm_o2_kpa_ == photo_temp_cache_atm_o2_kpa_) { - // Cache hit (non-PM): temperature params unchanged; only electron_transport_ + photo_key == photo_temp_cache_key_) { + // Cache hit (non-PM): every input unchanged; only electron_transport_ // depends on the per-call PPFD_, so refresh just that (as before). electron_transport_ = electron_transport(); } else { update_temperature_dependent_params(leaf_temp_); - photo_temp_cache_leaf_temp_ = leaf_temp_; - photo_temp_cache_atm_o2_kpa_ = atm_o2_kpa_; + photo_temp_cache_key_ = photo_key; photo_temp_cached_ = true; } @@ -2382,12 +2428,31 @@ inline double Leaf::peak_arrh_curve(double Ea, double ref_value, double leaf_tem // depends on the per-call PPFD_ and is (re)computed here from the just-updated // jmax_ -- on the non-PM cache-hit path set_physiology refreshes it separately. // -// ⚠️ R_d INHERITS VCMAX'S PEAKED CURVE AND SO FALLS ABOVE THE THERMAL OPTIMUM, -// where dark respiration should rise. Matched at 25 C against a Q10 of 2, the -// two diverge in opposite directions: at 25/35/40/45/50 C this gives 0.395, -// 0.543, 0.466, 0.284, 0.135 against the Q10's 0.395, 0.790, 1.117, 1.580, -// 2.234 -- a factor of 16.5 apart by 50 C, and moving the wrong way. See the -// note at the R_d_ assignment below for why it is recorded rather than changed. +// R_d comes from R_d_25 and the declining Q10, so it RISES with temperature. +// It used to be a fraction of vcmax_(T) and therefore fell above the thermal +// optimum, which was the wrong direction (#41). + +// Every scalar update_temperature_dependent_params() below reads, in one place so +// the cache key and the computation cannot drift apart. +// +// ⚠️ KEEP THIS IMMEDIATELY ABOVE THAT FUNCTION AND IN STEP WITH IT. Adding an input +// there without adding it here reintroduces exactly the silent staleness this key +// exists to remove -- the fit still converges and the numbers stay plausible. +// `photo_temp_key_size` is the guard: the compiler rejects a mismatched list. +// +// Bit equality (`==`) is the right comparison. The question is "did any input +// change", not "did it change materially": an input that moved by one ULP produces +// a different response and must invalidate. +inline std::array Leaf::photo_temp_key() const { + return {leaf_temp_, atm_o2_kpa_, + vcmax_25, vcmax_ha_, vcmax_H_d_, vcmax_d_S_, + jmax_25, jmax_ha_, jmax_H_d_, jmax_d_S_, + gamma_25_, gamma_ha_, + kc_25_, kc_ha_, + ko_25_, ko_ha_, + R_d_25, rd_q10_intercept_, rd_q10_slope_}; +} + inline void Leaf::update_temperature_dependent_params(double leaf_temp) { vcmax_ = peak_arrh_curve(vcmax_ha_, vcmax_25, leaf_temp, vcmax_H_d_, vcmax_d_S_); @@ -2395,24 +2460,19 @@ inline void Leaf::update_temperature_dependent_params(double leaf_temp) { gamma_ = arrh_curve(gamma_ha_, gamma_25_, leaf_temp); ko_ = arrh_curve(ko_ha_, ko_25_, leaf_temp); kc_ = arrh_curve(kc_ha_, kc_25_, leaf_temp); - // ⚠️ RESPIRATION INHERITS VCMAX'S PEAKED CURVE, SO IT FALLS ABOVE THE THERMAL - // OPTIMUM. That is wrong: dark respiration rises with temperature over this - // range, and a Q10 near 2 is the standard description. Tying R_d to vcmax_(T) - // -- which is what this line does -- makes it peak wherever Vcmax peaks and - // decline after. It diverges from a Q10 of 2 in the opposite direction and by - // an order of magnitude by 50 C -- the numbers are tabulated in this - // function's doc block above, rather than here, because an indented block - // inside a function body is what Doxygen 1.9 on CI rejects. - // - // No value of rd_to_vcmax_ratio_ repairs this -- it is a scale on a function - // of the wrong shape. It matters most for anything studying high-temperature - // behaviour, because understating respiration above the optimum understates - // how fast NET assimilation declines there. - // - // Left as-is rather than changed unilaterally: R_d feeds every operating point - // and the golden file, so switching to a Q10 moves published plant results and - // needs its own change with its own measured blast radius. - R_d_ = vcmax_ * rd_to_vcmax_ratio_; + // Respiration RISES with temperature, on the declining Q10 above. ⚠️ It is + // exactly R_d_25 at 25 C and larger above, so any check taken at 25 C alone is + // blind to this whole response -- test_rd_temperature_response is what covers it. + // + // Fail rather than fall back: R_d_25 is a trait, and an unset one is a caller + // error, not a cue to derive something from vcmax. + if (!std::isfinite(R_d_25) || R_d_25 < 0.0) { + util::stop("R_d_25 must be a finite, non-negative dark respiration at 25 C; " + "got " + util::format_double(R_d_25)); + } + const double q10 = + rd_q10_intercept_ - rd_q10_slope_ * (leaf_temp + 25.0) / 2.0; + R_d_ = R_d_25 * std::pow(q10, (leaf_temp - 25.0) / 10.0); km_ = (kc_*umol_per_mol_to_Pa_)*(1 + (atm_o2_kpa_*kPa_to_Pa)/(ko_*umol_per_mol_to_Pa_)); electron_transport_ = electron_transport(); } @@ -2817,18 +2877,34 @@ inline double Leaf::psi_stem_to_ci(double psi_stem, double psi_upstream) { try { return ci_ = util::uniroot_smooth(target, gamma_ * umol_per_mol_to_Pa_, ca_, 1e-10, ci_niter); } catch (const std::exception& e) { - // Penman-Monteith path (#523): extreme energy-balance leaf heating raises the - // CO2 compensation point (gamma*) so far that assimilation is negative across - // the whole [gamma*, ca] bracket, so there is no supply==demand root and - // TOMS748 cannot bracket. That is a physically-meaningful shut-down (the leaf - // is too hot to gain carbon), not a solver failure, so operate at the - // compensation point (ci = gamma*, gross A = 0, net A = -R_d) and let the - // profit optimiser move away from it. Gated on use_energy_balance_ so the - // non-PM path keeps its original fail-fast contract (it never reaches here - // under prescribed leaf_temp). - if (use_energy_balance_) { + // Assimilation can be negative across the WHOLE [gamma*, ca] bracket -- the + // leaf is too hot to gain carbon at any internal CO2 -- and then there is no + // supply==demand root at all. That is a physically-meaningful shut-down, not a + // solver failure: operate at the compensation point (ci = gamma*, gross A = 0, + // net A = -R_d) and let the profit optimiser move away from it. + // + // ⚠️ THIS USED TO BE GATED ON use_energy_balance_, on the grounds that the + // prescribed-temperature path "never reaches here". That was true and #41 made + // it false: raising R_d to a Q10 response is enough to drive assimilation + // negative throughout by ~45 C at the defaults, and the prescribed path then + // threw where the PM path shut down -- the same physics, two different + // outcomes, decided by how leaf_temp happened to be obtained. + // + // ⚠️ THE GATE IS NOT SIMPLY REMOVED, because that would mask real solver + // failures as shut-downs: this `catch` sees ANY exception from the root-find, + // and fail-fast has value. The target is strictly monotone over (gamma*, ca] + // (#486), so "no root exists" is distinguishable from "the solver broke" by + // the sign at the two ends -- equal signs means the root is genuinely outside + // the bracket. Only that case shuts down; anything else still stops. + const double lo = gamma_ * umol_per_mol_to_Pa_; + const double t_lo = target(lo); + const double t_hi = target(ca_); + const bool no_root_in_bracket = + std::isfinite(t_lo) && std::isfinite(t_hi) && + ((t_lo > 0.0 && t_hi > 0.0) || (t_lo < 0.0 && t_hi < 0.0)); + if (use_energy_balance_ || no_root_in_bracket) { ci_at_compensation_point_ = true; - return ci_ = gamma_ * umol_per_mol_to_Pa_; + return ci_ = lo; } util::stop("psi_stem_to_ci failed: " + std::string(e.what()) + "; min=" + util::to_string(gamma_ * umol_per_mol_to_Pa_) + diff --git a/man/leaf_gradient.Rd b/man/leaf_gradient.Rd index 1e88746..21bd86c 100644 --- a/man/leaf_gradient.Rd +++ b/man/leaf_gradient.Rd @@ -70,10 +70,14 @@ differentiate at} \item{supply}{how water reaches the root collar: [leaf_supply_multilayer()] (the default) or [leaf_supply_single()]} -\item{pars}{what to differentiate with respect to. Any of the thirteen +\item{pars}{what to differentiate with respect to. Any of the fourteen [leaf_traits()] names, plus `"leaf_specific_conductance_max"` and — on the single-potential path only — `"resistance"`. Defaults to all of them. + `dY/dvcmax_25` is a PARTIAL at fixed respiration: `R_d_25` is its own trait, + so a fit that wants respiration to follow Vcmax moves both and adds the two + columns. + `beta_R_H` and `beta_R_V` were here until #33 and are not any more: they parameterise the root-architecture model, which the leaf no longer runs, so this function has no way to reach them. Getting a gradient in either means @@ -236,9 +240,9 @@ The companion study `leaf-calibration` has `N = 1327`, `P_fit = 40`, 57-parameter variant costing the same as its 40-parameter one, because `P_model` is 4 in both. -⚠️ **Always pass `pars`.** It is `P_model`, so the default — all fourteen on +⚠️ **Always pass `pars`.** It is `P_model`, so the default — all fifteen on the multi-layer path — is the most expensive thing you can ask for, and a fit -that reads four of them pays for ten it discards. +that reads four of them pays for eleven it discards. The intercept is a fresh `Leaf` per call, which there is currently no way to avoid (see phylloptim#52); it is 29% of the exact gradient in the study above. diff --git a/man/leaf_traits.Rd b/man/leaf_traits.Rd index 1207382..e585574 100644 --- a/man/leaf_traits.Rd +++ b/man/leaf_traits.Rd @@ -17,7 +17,8 @@ leaf_traits( a = 0.3, curv_fact_elec_trans = 0.7, curv_fact_colim = 0.99, - cost_scale_TF24 = 7.5 + cost_scale_TF24 = 7.5, + R_d_25 = 1.44 ) } \arguments{ @@ -47,6 +48,9 @@ leaf_traits( \item{cost_scale_TF24}{cost parameter for the TF24 profit model (umol m^-2 s^-1)} + +\item{R_d_25}{dark respiration at 25 C (umol m^-2 s^-1). It is the value at +25 C only: respiration rises from there on Tjoelker's declining-Q10 curve.} } \value{ A `leaf_traits` object; a named list. diff --git a/man/set_traits.Rd b/man/set_traits.Rd index 5d1ea42..6dd2ccd 100644 --- a/man/set_traits.Rd +++ b/man/set_traits.Rd @@ -27,7 +27,7 @@ be called before the next solve. That is not caution: `vcmax_`, `jmax_` and `R_d_` are derived from the traits inside `set_physiology()`, so they are genuinely unknown until the drivers are re-supplied. -The reason it is a function rather than thirteen assignable fields is that +The reason it is a function rather than fourteen assignable fields is that `leaf$vcmax_25 <- x` could not be made correct. Three separate pieces of derived state go stale on a bare trait write: the two pre-integrated vulnerability splines, the solved operating point, and -- least visibly -- diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 81298b7..a086b7e 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -103,8 +103,8 @@ BEGIN_RCPP END_RCPP } // Leaf__set_traits -void Leaf__set_traits(phylloptim::RcppR6::RcppR6 obj_, double vcmax_25, double stem_c, double stem_b, double psi_crit, double root_c, double root_b, double root_psi_crit, double beta2, double jmax_25, double a, double curv_fact_elec_trans, double curv_fact_colim, double cost_scale_TF24); -RcppExport SEXP _phylloptim_Leaf__set_traits(SEXP obj_SEXP, SEXP vcmax_25SEXP, SEXP stem_cSEXP, SEXP stem_bSEXP, SEXP psi_critSEXP, SEXP root_cSEXP, SEXP root_bSEXP, SEXP root_psi_critSEXP, SEXP beta2SEXP, SEXP jmax_25SEXP, SEXP aSEXP, SEXP curv_fact_elec_transSEXP, SEXP curv_fact_colimSEXP, SEXP cost_scale_TF24SEXP) { +void Leaf__set_traits(phylloptim::RcppR6::RcppR6 obj_, double vcmax_25, double stem_c, double stem_b, double psi_crit, double root_c, double root_b, double root_psi_crit, double beta2, double jmax_25, double a, double curv_fact_elec_trans, double curv_fact_colim, double cost_scale_TF24, double R_d_25); +RcppExport SEXP _phylloptim_Leaf__set_traits(SEXP obj_SEXP, SEXP vcmax_25SEXP, SEXP stem_cSEXP, SEXP stem_bSEXP, SEXP psi_critSEXP, SEXP root_cSEXP, SEXP root_bSEXP, SEXP root_psi_critSEXP, SEXP beta2SEXP, SEXP jmax_25SEXP, SEXP aSEXP, SEXP curv_fact_elec_transSEXP, SEXP curv_fact_colimSEXP, SEXP cost_scale_TF24SEXP, SEXP R_d_25SEXP) { BEGIN_RCPP Rcpp::RNGScope rcpp_rngScope_gen; Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); @@ -121,7 +121,8 @@ BEGIN_RCPP Rcpp::traits::input_parameter< double >::type curv_fact_elec_trans(curv_fact_elec_transSEXP); Rcpp::traits::input_parameter< double >::type curv_fact_colim(curv_fact_colimSEXP); Rcpp::traits::input_parameter< double >::type cost_scale_TF24(cost_scale_TF24SEXP); - Leaf__set_traits(obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24); + Rcpp::traits::input_parameter< double >::type R_d_25(R_d_25SEXP); + Leaf__set_traits(obj_, vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25); return R_NilValue; END_RCPP } @@ -1328,25 +1329,69 @@ BEGIN_RCPP return R_NilValue; END_RCPP } -// Leaf__rd_to_vcmax_ratio___get -double Leaf__rd_to_vcmax_ratio___get(phylloptim::RcppR6::RcppR6 obj_); -RcppExport SEXP _phylloptim_Leaf__rd_to_vcmax_ratio___get(SEXP obj_SEXP) { +// Leaf__R_d_25__get +double Leaf__R_d_25__get(phylloptim::RcppR6::RcppR6 obj_); +RcppExport SEXP _phylloptim_Leaf__R_d_25__get(SEXP obj_SEXP) { BEGIN_RCPP Rcpp::RObject rcpp_result_gen; Rcpp::RNGScope rcpp_rngScope_gen; Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); - rcpp_result_gen = Rcpp::wrap(Leaf__rd_to_vcmax_ratio___get(obj_)); + rcpp_result_gen = Rcpp::wrap(Leaf__R_d_25__get(obj_)); return rcpp_result_gen; END_RCPP } -// Leaf__rd_to_vcmax_ratio___set -void Leaf__rd_to_vcmax_ratio___set(phylloptim::RcppR6::RcppR6 obj_, double value); -RcppExport SEXP _phylloptim_Leaf__rd_to_vcmax_ratio___set(SEXP obj_SEXP, SEXP valueSEXP) { +// Leaf__R_d_25__set +void Leaf__R_d_25__set(phylloptim::RcppR6::RcppR6 obj_, double value); +RcppExport SEXP _phylloptim_Leaf__R_d_25__set(SEXP obj_SEXP, SEXP valueSEXP) { BEGIN_RCPP Rcpp::RNGScope rcpp_rngScope_gen; Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); Rcpp::traits::input_parameter< double >::type value(valueSEXP); - Leaf__rd_to_vcmax_ratio___set(obj_, value); + Leaf__R_d_25__set(obj_, value); + return R_NilValue; +END_RCPP +} +// Leaf__rd_q10_intercept___get +double Leaf__rd_q10_intercept___get(phylloptim::RcppR6::RcppR6 obj_); +RcppExport SEXP _phylloptim_Leaf__rd_q10_intercept___get(SEXP obj_SEXP) { +BEGIN_RCPP + Rcpp::RObject rcpp_result_gen; + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); + rcpp_result_gen = Rcpp::wrap(Leaf__rd_q10_intercept___get(obj_)); + return rcpp_result_gen; +END_RCPP +} +// Leaf__rd_q10_intercept___set +void Leaf__rd_q10_intercept___set(phylloptim::RcppR6::RcppR6 obj_, double value); +RcppExport SEXP _phylloptim_Leaf__rd_q10_intercept___set(SEXP obj_SEXP, SEXP valueSEXP) { +BEGIN_RCPP + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); + Rcpp::traits::input_parameter< double >::type value(valueSEXP); + Leaf__rd_q10_intercept___set(obj_, value); + return R_NilValue; +END_RCPP +} +// Leaf__rd_q10_slope___get +double Leaf__rd_q10_slope___get(phylloptim::RcppR6::RcppR6 obj_); +RcppExport SEXP _phylloptim_Leaf__rd_q10_slope___get(SEXP obj_SEXP) { +BEGIN_RCPP + Rcpp::RObject rcpp_result_gen; + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); + rcpp_result_gen = Rcpp::wrap(Leaf__rd_q10_slope___get(obj_)); + return rcpp_result_gen; +END_RCPP +} +// Leaf__rd_q10_slope___set +void Leaf__rd_q10_slope___set(phylloptim::RcppR6::RcppR6 obj_, double value); +RcppExport SEXP _phylloptim_Leaf__rd_q10_slope___set(SEXP obj_SEXP, SEXP valueSEXP) { +BEGIN_RCPP + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< phylloptim::RcppR6::RcppR6 >::type obj_(obj_SEXP); + Rcpp::traits::input_parameter< double >::type value(valueSEXP); + Leaf__rd_q10_slope___set(obj_, value); return R_NilValue; END_RCPP } @@ -2199,7 +2244,7 @@ static const R_CallMethodDef CallEntries[] = { {"_phylloptim_Leaf__initialize_integrator", (DL_FUNC) &_phylloptim_Leaf__initialize_integrator, 3}, {"_phylloptim_Leaf__set_physiology", (DL_FUNC) &_phylloptim_Leaf__set_physiology, 11}, {"_phylloptim_Leaf__perturb_stem_b", (DL_FUNC) &_phylloptim_Leaf__perturb_stem_b, 2}, - {"_phylloptim_Leaf__set_traits", (DL_FUNC) &_phylloptim_Leaf__set_traits, 14}, + {"_phylloptim_Leaf__set_traits", (DL_FUNC) &_phylloptim_Leaf__set_traits, 15}, {"_phylloptim_Leaf__proportion_of_conductivity", (DL_FUNC) &_phylloptim_Leaf__proportion_of_conductivity, 2}, {"_phylloptim_Leaf__arrh_curve", (DL_FUNC) &_phylloptim_Leaf__arrh_curve, 4}, {"_phylloptim_Leaf__peak_arrh_curve", (DL_FUNC) &_phylloptim_Leaf__peak_arrh_curve, 6}, @@ -2306,8 +2351,12 @@ static const R_CallMethodDef CallEntries[] = { {"_phylloptim_Leaf__ko_25___set", (DL_FUNC) &_phylloptim_Leaf__ko_25___set, 2}, {"_phylloptim_Leaf__ko_ha___get", (DL_FUNC) &_phylloptim_Leaf__ko_ha___get, 1}, {"_phylloptim_Leaf__ko_ha___set", (DL_FUNC) &_phylloptim_Leaf__ko_ha___set, 2}, - {"_phylloptim_Leaf__rd_to_vcmax_ratio___get", (DL_FUNC) &_phylloptim_Leaf__rd_to_vcmax_ratio___get, 1}, - {"_phylloptim_Leaf__rd_to_vcmax_ratio___set", (DL_FUNC) &_phylloptim_Leaf__rd_to_vcmax_ratio___set, 2}, + {"_phylloptim_Leaf__R_d_25__get", (DL_FUNC) &_phylloptim_Leaf__R_d_25__get, 1}, + {"_phylloptim_Leaf__R_d_25__set", (DL_FUNC) &_phylloptim_Leaf__R_d_25__set, 2}, + {"_phylloptim_Leaf__rd_q10_intercept___get", (DL_FUNC) &_phylloptim_Leaf__rd_q10_intercept___get, 1}, + {"_phylloptim_Leaf__rd_q10_intercept___set", (DL_FUNC) &_phylloptim_Leaf__rd_q10_intercept___set, 2}, + {"_phylloptim_Leaf__rd_q10_slope___get", (DL_FUNC) &_phylloptim_Leaf__rd_q10_slope___get, 1}, + {"_phylloptim_Leaf__rd_q10_slope___set", (DL_FUNC) &_phylloptim_Leaf__rd_q10_slope___set, 2}, {"_phylloptim_Leaf__PPFD___get", (DL_FUNC) &_phylloptim_Leaf__PPFD___get, 1}, {"_phylloptim_Leaf__PPFD___set", (DL_FUNC) &_phylloptim_Leaf__PPFD___set, 2}, {"_phylloptim_Leaf__atm_vpd___get", (DL_FUNC) &_phylloptim_Leaf__atm_vpd___get, 1}, diff --git a/src/RcppR6.cpp b/src/RcppR6.cpp index fa1d0db..f83f997 100644 --- a/src/RcppR6.cpp +++ b/src/RcppR6.cpp @@ -28,8 +28,8 @@ void Leaf__perturb_stem_b(phylloptim::RcppR6::RcppR6 obj_, dou obj_->perturb_stem_b(stem_b); } // [[Rcpp::export]] -void Leaf__set_traits(phylloptim::RcppR6::RcppR6 obj_, double vcmax_25, double stem_c, double stem_b, double psi_crit, double root_c, double root_b, double root_psi_crit, double beta2, double jmax_25, double a, double curv_fact_elec_trans, double curv_fact_colim, double cost_scale_TF24) { - obj_->set_traits(vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24); +void Leaf__set_traits(phylloptim::RcppR6::RcppR6 obj_, double vcmax_25, double stem_c, double stem_b, double psi_crit, double root_c, double root_b, double root_psi_crit, double beta2, double jmax_25, double a, double curv_fact_elec_trans, double curv_fact_colim, double cost_scale_TF24, double R_d_25) { + obj_->set_traits(vcmax_25, stem_c, stem_b, psi_crit, root_c, root_b, root_psi_crit, beta2, jmax_25, a, curv_fact_elec_trans, curv_fact_colim, cost_scale_TF24, R_d_25); } // [[Rcpp::export]] double Leaf__proportion_of_conductivity(phylloptim::RcppR6::RcppR6 obj_, double psi) { @@ -492,12 +492,30 @@ void Leaf__ko_ha___set(phylloptim::RcppR6::RcppR6 obj_, double } // [[Rcpp::export]] -double Leaf__rd_to_vcmax_ratio___get(phylloptim::RcppR6::RcppR6 obj_) { - return obj_->rd_to_vcmax_ratio_; +double Leaf__R_d_25__get(phylloptim::RcppR6::RcppR6 obj_) { + return obj_->R_d_25; } // [[Rcpp::export]] -void Leaf__rd_to_vcmax_ratio___set(phylloptim::RcppR6::RcppR6 obj_, double value) { - obj_->rd_to_vcmax_ratio_ = value; +void Leaf__R_d_25__set(phylloptim::RcppR6::RcppR6 obj_, double value) { + obj_->R_d_25 = value; +} + +// [[Rcpp::export]] +double Leaf__rd_q10_intercept___get(phylloptim::RcppR6::RcppR6 obj_) { + return obj_->rd_q10_intercept_; +} +// [[Rcpp::export]] +void Leaf__rd_q10_intercept___set(phylloptim::RcppR6::RcppR6 obj_, double value) { + obj_->rd_q10_intercept_ = value; +} + +// [[Rcpp::export]] +double Leaf__rd_q10_slope___get(phylloptim::RcppR6::RcppR6 obj_) { + return obj_->rd_q10_slope_; +} +// [[Rcpp::export]] +void Leaf__rd_q10_slope___set(phylloptim::RcppR6::RcppR6 obj_, double value) { + obj_->rd_q10_slope_ = value; } // [[Rcpp::export]] diff --git a/src/gradient.cpp b/src/gradient.cpp index 791bbe2..cbcedce 100644 --- a/src/gradient.cpp +++ b/src/gradient.cpp @@ -55,13 +55,13 @@ DriverBatch* checked(SEXP drivers) { //' The differentiable parameters, in the order C++ indexes them //' -//' The thirteen [leaf_traits()] in `set_traits()`'s argument order, then +//' The fourteen [leaf_traits()] in `set_traits()`'s argument order, then //' `leaf_specific_conductance_max` and `resistance`. Exported so that R's own //' copy of this order can be compared against it in a test: R passes integer //' positions into this enumeration, so appending to it is safe and reordering it //' would silently differentiate the wrong parameter. //' -//' @return A character vector of fifteen names. +//' @return A character vector of sixteen names. //' @seealso [leaf_gradient_batch()] //' @examples //' gradient_par_names() diff --git a/tests/cpp/bench_gradient.cpp b/tests/cpp/bench_gradient.cpp index 641a692..ea294a3 100644 --- a/tests/cpp/bench_gradient.cpp +++ b/tests/cpp/bench_gradient.cpp @@ -12,8 +12,8 @@ // distinction matters because **plant links these headers directly**. So the // arithmetic has to be done again with the boundary removed, which is what this // measures. PLAN 11e records the answer; the short version is that the composite -// does win here, by rather less than 12x, and for four of the fifteen traits by -// almost nothing at all -- for a reason neither 11d nor 11e anticipated. +// does win here, by rather less than 12x, and for four of the traits by almost +// nothing at all -- for a reason neither 11d nor 11e anticipated. // // WHAT THE TWO ARMS ARE. Both perturb one trait by a relative 1e-6 either side // and both pay set_traits + set_physiology per perturbation, because a trait @@ -55,11 +55,13 @@ namespace { // The default trait vector, in set_traits' argument order. -// Thirteen, not fifteen: beta_R_H and beta_R_V left with the root-architecture -// model in #33. They were two of the four traits whose gradient is 100% -// argmax-mediated, and a gradient in either is now taken where the network is -// built -- exactly, because root_network_from_carbon is homogeneous of degree 1 -// in each. +// +// Thirteen of the fourteen traits: `R_d_25` is left at its default because it needs +// no spline rebuild and so lands in the cheap bucket, which the split below already +// has twelve examples of. `beta_R_H` and `beta_R_V` are not here at all -- they left +// with the root-architecture model in #33, and a gradient in either is now taken +// where the network is built, exactly, because root_network_from_carbon is +// homogeneous of degree 1 in each. struct Traits { double v[13]; }; @@ -81,8 +83,10 @@ bool rebuilds_a_spline(int i) { } void apply_traits(phylloptim::Leaf &l, const Traits &t) { + // R_d_25 last, at the class default, so the benchmark measures the default + // configuration. l.set_traits(t.v[0], t.v[1], t.v[2], t.v[3], t.v[4], t.v[5], t.v[6], t.v[7], - t.v[8], t.v[9], t.v[10], t.v[11], t.v[12]); + t.v[8], t.v[9], t.v[10], t.v[11], t.v[12], 1.44); } // One interior operating point. Drivers from plant's tests/testthat/test-leaf.r, @@ -274,7 +278,7 @@ int main(int argc, char **argv) { } } - printf("\n all 13 traits FD %8.1f us IFT %8.1f us %.2fx\n", + printf("\n 13 of the 14 traits FD %8.1f us IFT %8.1f us %.2fx\n", fd_all, ift_all, fd_all / ift_all); printf(" the %2d with no rebuild FD %8.1f us IFT %8.1f us %.2fx\n", n_cheap, fd_cheap, ift_cheap, fd_cheap / ift_cheap); diff --git a/tests/cpp/bench_solve.cpp b/tests/cpp/bench_solve.cpp index 8579b26..9b557e9 100644 --- a/tests/cpp/bench_solve.cpp +++ b/tests/cpp/bench_solve.cpp @@ -8,9 +8,15 @@ // kept because the question recurs (issue #3 asks the same thing about lambda, // and gets a different answer). // -// Workload is the golden-file grid: 288 operating points over psi_soil, PPFD, -// VPD and 1/3/5 soil layers, i.e. the same state space the regression baseline -// covers, shutdown corner included. +// Workload is 288 operating points over psi_soil, PPFD, VPD and 1/3/5 soil layers, +// all at a leaf temperature of 25 C, shutdown corner included -- the golden grid's +// state axes, at its reference temperature. +// +// ⚠️ It deliberately does NOT follow the golden grid's temperature axis. A timing +// baseline is only useful against its own history (tools/cost-baseline.tsv, +// tools/bench_history.sh), so doubling the workload would end that history to +// measure nothing new about the solve. If a temperature-dependent cost ever needs +// measuring, add a second workload rather than growing this one. // // Reports min-of-N, not mean. This is a deterministic computation on a noisy // machine, so the minimum is the least-contaminated estimate of its cost; the diff --git a/tests/cpp/golden/operating_points.tsv b/tests/cpp/golden/operating_points.tsv index 2191e6a..5941004 100644 --- a/tests/cpp/golden/operating_points.tsv +++ b/tests/cpp/golden/operating_points.tsv @@ -1,289 +1,577 @@ -psi_soil ppfd vpd layers psi_stem opt_root_psi ci assim transpiration gc profit e_up uptake -0.5 100 0.5 1 1.4064315157230882 1.1397291800324882 33.535719423557353 3.4216414573490117 7.9644452142332409e-06 0.053619621786311598 3.3030570555526011 7.9644455320981397e-06 0.00044210077891191453 -0.5 100 0.5 3 1.5954124971659938 1.4018117298270372 31.191249087006778 3.2939585898339492 5.626586940336478e-06 0.037880286143406806 3.1008759409911337 5.6265870700498372e-06 0.00031232789731056547 -0.5 100 0.5 5 1.7452545545113238 1.5881353349338942 29.262213724659755 3.1770775521522618 4.4519911133823881e-06 0.029972468046986948 2.9051006149550638 4.4519915504116376e-06 0.00024712692480775118 -0.5 100 1 1 1.5932824843611644 1.2671223542432735 29.879407846846796 3.2157448245139046 9.5619590523274174e-06 0.032187340996817596 3.023650171377644 9.5619591422393007e-06 0.00053077763764858732 -0.5 100 1 3 1.7920899362273437 1.5523575254639288 26.688926403109683 3.0013314142961085 6.7853474838497329e-06 0.022840747596739566 2.7006930858511775 6.7853474843817848e-06 0.00037664987423712378 -0.5 100 1 5 1.9404992363787317 1.7453156059561379 24.22920998828554 2.8076762493713701 5.3575323613880757e-06 0.018034455081201134 2.402599334908301 5.357532576432653e-06 0.00029739287129795463 -0.5 100 2 1 1.7967548832244611 1.4030643672663468 24.763245420986252 2.8521396964186123 1.1266254056967917e-05 0.018962158230542741 2.5485370769014066 1.126625410728482e-05 0.000625381854414922 -0.5 100 2 3 1.974750501718451 1.6895987603563785 20.874909545225634 2.4917019650291854 7.8414037562845282e-06 0.013197815176578424 2.0594485162722274 7.8414043294004221e-06 0.00043527084814878831 -0.5 100 2 5 2.0812347115368164 1.8568575136921954 18.155583441976756 2.1776498358393557 5.9999663789796766e-06 0.010098504017471864 1.6531924903518367 5.9999667351424357e-06 0.00033305394033541135 -0.5 100 4 1 1.9478356888215389 1.5017496970624489 18.554034088544238 2.22758211566109 1.2503146687341704e-05 0.010521982047725396 1.8167837670905369 1.2503147133216513e-05 0.00069404091774723914 -0.5 100 4 3 2.0130156381644118 1.7179877325704682 14.788296988437251 1.6880916255969947 8.0598145297856256e-06 0.0067827104577008772 1.2240623501463719 8.0598148848335275e-06 0.00044739466471460052 -0.5 100 4 5 2.0063215670071219 1.7976840658200521 12.604399811198828 1.2879603966247419 5.6591721458135337e-06 0.0047624577406199832 0.82959875184286114 5.6591722813330852e-06 0.00031413667950780377 -0.5 500 0.5 1 2.4109901172055332 1.7891385804115791 26.953803399175349 13.96235023623394 1.6103335350584414e-05 0.10841367198476044 13.074476999673427 1.610333535121711e-05 0.00089388483770286482 -0.5 500 0.5 3 2.7164829891259941 2.210510814002963 23.551280527047581 12.950185456809166 1.1846365343788493e-05 0.079754158913824647 11.617786198957624 1.1846366710650622e-05 0.00065758349767697038 -0.5 500 0.5 5 2.9416567539754097 2.4917986705441106 21.156049380602255 12.089414780959613 9.6532721227130728e-06 0.064989435710501212 10.366287275475118 9.6532733143316879e-06 0.00053584642322129826 -0.5 500 1 1 2.7771547107039529 1.9960803050999476 20.778763228621415 11.939993582679428 1.8693644905798969e-05 0.06292630200188086 10.507323310430499 1.8693645986015445e-05 0.0010376711621435163 -0.5 500 1 3 3.0330102014270279 2.4086469007774403 17.044362096255803 10.197210725093214 1.3367901976215948e-05 0.044998856088571453 8.3018317586369506 1.3367901981828912e-05 0.00074204285216924299 -0.5 500 1 5 3.158329436174887 2.6343326757148198 14.72304159230254 8.7962094107062914 1.0472297472006299e-05 0.035251710230816372 6.6531341193001641 1.0472298027026705e-05 0.00058130990990989202 -0.5 500 2 1 2.9462904096973768 2.0844428808493811 14.248433530867084 8.4712366920423499 1.9799051423878981e-05 0.033323653453567317 6.73955249947117 1.979905230028143e-05 0.0010990314904402681 -0.5 500 2 3 2.9225815548173313 2.341499812224078 11.30988163184572 6.1265377221242154 1.2852392837172094e-05 0.021631777997126112 4.4384260644956619 1.2852394389878225e-05 0.00071342738772568553 -0.5 500 2 5 2.8331109150616167 2.4173177253909577 9.7364229966751275 4.6386409369409947 9.2251134932391925e-06 0.015526727949590972 3.1101510785484425 9.2251137575675636e-06 0.00051207958687580146 -0.5 500 4 1 2.6402150326898228 1.9210741314244792 9.583691352196416 4.4863829806344775 1.7755015392816997e-05 0.014941674915279099 3.2745250391091165 1.7755016415853437e-05 0.00098556849380257764 -0.5 500 4 3 2.436356190059195 2.0218974856044101 7.9399765537701912 2.7690999438141009 1.039695131715295e-05 0.0087495202484437189 1.8482539356547498 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5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 +6 1500 4 40 1 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 +6 1500 4 40 3 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 +6 1500 4 40 5 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 diff --git a/tests/cpp/test_golden.cpp b/tests/cpp/test_golden.cpp index 84087de..eaec452 100644 --- a/tests/cpp/test_golden.cpp +++ b/tests/cpp/test_golden.cpp @@ -44,7 +44,7 @@ const char *kGoldenPath = "golden/operating_points.tsv"; struct Row { // inputs - double psi_soil, ppfd, vpd; + double psi_soil, ppfd, vpd, leaf_temp; int layers; // outputs double psi_stem, opt_root_psi, ci, assim, transpiration, gc, profit, e_up, uptake; @@ -58,9 +58,19 @@ struct Row { // Trait values and fixed drivers from plant's tests/testthat/test-leaf.r. const double kTheta = 0.000157, kKs = 1.0, kH = 5.0; const double kAreaLeaf = 0.05; -const double kCa = 40.0, kO2 = 21.0, kTleaf = 25.0, kPatm = 101.3; +const double kCa = 40.0, kO2 = 21.0, kPatm = 101.3; +// ⚠️ LEAF TEMPERATURE IS A GRID AXIS, NOT A FIXED DRIVER. It was fixed at 25 C, and +// that made this file blind to every temperature response in the model: the +// reference values of Vcmax, Jmax and R_d are DEFINED at 25 C, so a change to any +// response curve is inert there BY CONSTRUCTION. +// +// Two temperatures are enough to see one: the reference, and 40 C where the response +// bites hardest. The extra pinned rows at the hot end are a feature rather than +// noise. +const double kLeafTemps[] = {25.0, 40.0}; -Row solve(double psi_soil, double ppfd, double vpd, int layers) { +Row solve(double psi_soil, double ppfd, double vpd, int layers, + double leaf_temp) { phylloptim::Leaf l; l.setup_transpiration(100); l.setup_root_vulnerability(100); @@ -76,7 +86,7 @@ Row solve(double psi_soil, double ppfd, double vpd, int layers) { } l.set_physiology(fixture::root_network(root, depth), ppfd, ps, depth, kKs * kTheta / kH, vpd, kCa, - kTleaf, kO2, kPatm); + leaf_temp, kO2, kPatm); l.find_root_collar_psi(); double uptake = 0.0; @@ -85,7 +95,8 @@ Row solve(double psi_soil, double ppfd, double vpd, int layers) { uptake += s; } } - return Row{psi_soil, ppfd, vpd, layers, l.opt_psi_stem_, + return Row{psi_soil, ppfd, vpd, leaf_temp, layers, + l.opt_psi_stem_, l.opt_root_psi_, l.ci_, l.assim_colimited_, l.transpiration_, l.stom_cond_CO2_, l.profit_, l.E_up_, uptake, l.operating_point_kind()}; @@ -97,12 +108,19 @@ std::vector run_grid() { const double vpds[] = {0.5, 1.0, 2.0, 4.0}; const int layer_counts[] = {1, 3, 5}; + // ⚠️ TEMPERATURE IS THE OUTERMOST LOOP ON PURPOSE. It makes the file contiguous + // copies of one 288-point state grid, so a regeneration that only adds a + // temperature is checkable as an ADDITION: the 25 C block must come out + // byte-identical. Reordering these loops rewrites every row without changing any + // value. std::vector rows; - for (double p : psi_soils) { - for (double q : ppfds) { - for (double d : vpds) { - for (int n : layer_counts) { - rows.push_back(solve(p, q, d, n)); + for (double t : kLeafTemps) { + for (double p : psi_soils) { + for (double q : ppfds) { + for (double d : vpds) { + for (int n : layer_counts) { + rows.push_back(solve(p, q, d, n, t)); + } } } } @@ -116,11 +134,11 @@ std::vector run_grid() { // // `Leaf::operating_point_kind()` says which branch of the collar solve produced // the point, and the grid's split between those branches is already an -// established number: 240 of the 288 points are feasible, of which 198 sit at an -// interior profit maximum and 42 at a constrained optimum pinned to a bracket -// bound (24 wet, 18 dry); the remaining 48 shut down. Those figures were measured -// when PLAN 11a replaced the collar solver and are quoted in the developer guide -// and in maximise_profit_over_collar's own comment. +// established number AT 25 C: 240 of those 288 points are feasible, of which 198 sit +// at an interior profit maximum and 42 at a constrained optimum pinned to a bracket +// bound (24 wet, 18 dry); the remaining 48 shut down. Those figures are quoted in +// the developer guide and in maximise_profit_over_collar's own comment. The 40 C +// counts were measured when the axis was added. // // So this asserts the classification against numbers that already exist rather // than inventing reference values for it. It is a cheap test with a specific @@ -129,44 +147,70 @@ std::vector run_grid() { // not reproduce this split, because dprofit's shut-down sentinel is exactly 0.0 // and would move all 48 shutdown points into `interior`. // -// Three kinds are expected to be EMPTY here: `shade-death` because the grid's -// minimum assim_max_ is 3.71 (it is reached by light, not by drying); -// `solver-refused` and `non-finite-gradient` because both bracket endpoints -// admit a usable gradient on all 240 feasible rows. +// Three kinds are expected to be EMPTY here: `shade-death` because assim_max_ never +// gets there (it is reached by light, not by drying, and not by heat either at 40 C); +// `solver-refused` and `non-finite-gradient` because both bracket endpoints admit a +// usable gradient on every feasible row. +// +// ⚠️ The hot end does NOT reach the compensation-point exit either, which is worth +// knowing before reading the zeros as coverage: at the defaults that needs about +// 45 C. `test_rd_temperature_response` covers it. // // A zero counts for this grid, whose psi_soil values are {0.5, 1, 2, 3, 4, 6}, // and says nothing about the model. What the two failure branches do is checked // by test_collar_solve_refuses_rather_than_guessing in test_leaf.cpp. +// ⚠️ COUNTED PER TEMPERATURE, not over the whole grid: a single total would let +// points move between branches as the leaf warms and still add up. struct KindCount { phylloptim::Leaf::OperatingPointKind kind; int expected; }; +// One row per entry of kLeafTemps, in that order. +struct TempKinds { + double leaf_temp; + int interior, pinned_wet, pinned_dry, shutdown; +}; +// +// The split MOVES with temperature, in a direction that is physical: a hot leaf +// assimilates less and respires more, so it has less to gain from water and its +// optimum presses against the WET bound instead of the dry one. The 48 shut-down +// rows do not move, because there it is hydraulics rather than heat that forbids +// transpiration. +const TempKinds kExpectedKinds[] = { + {25.0, 198, 24, 18, 48}, + {40.0, 160, 80, 0, 48}, +}; + int check_operating_kinds(const std::vector &rows) { using Kind = phylloptim::Leaf::OperatingPointKind; - const KindCount expected[] = { - {Kind::Interior, 198}, {Kind::PinnedWet, 24}, - {Kind::PinnedDry, 18}, {Kind::HydraulicShutdown, 48}, - {Kind::Determined, 0}, {Kind::ShadeDeath, 0}, - {Kind::Prescribed, 0}, {Kind::SolverRefused, 0}, - {Kind::NonFiniteGradient, 0}, {Kind::Unsolved, 0}, - }; - int failures = 0; int classified = 0; - for (const KindCount &e : expected) { - int got = 0; - for (const Row &r : rows) { - if (r.kind == e.kind) { - ++got; + for (const TempKinds &e : kExpectedKinds) { + const KindCount expected[] = { + {Kind::Interior, e.interior}, + {Kind::PinnedWet, e.pinned_wet}, + {Kind::PinnedDry, e.pinned_dry}, + {Kind::HydraulicShutdown, e.shutdown}, + {Kind::Determined, 0}, {Kind::ShadeDeath, 0}, + {Kind::Prescribed, 0}, {Kind::SolverRefused, 0}, + {Kind::NonFiniteGradient, 0}, {Kind::Unsolved, 0}, + }; + for (const KindCount &k : expected) { + int got = 0; + for (const Row &r : rows) { + if (r.leaf_temp == e.leaf_temp && r.kind == k.kind) { + ++got; + } + } + classified += got; + if (got != k.expected) { + ++failures; + fprintf(stderr, "FAIL kinds at T=%g: %s got %d, expected %d\n", + e.leaf_temp, + phylloptim::Leaf::operating_point_kind_name(k.kind), got, + k.expected); } - } - classified += got; - if (got != e.expected) { - ++failures; - fprintf(stderr, "FAIL kinds: %s got %d, expected %d\n", - phylloptim::Leaf::operating_point_kind_name(e.kind), got, - e.expected); } } if (classified != static_cast(rows.size())) { @@ -175,19 +219,25 @@ int check_operating_kinds(const std::vector &rows) { rows.size()); } if (failures == 0) { - printf("kinds: %zu points -- 198 interior, 42 pinned (24 wet, 18 dry), " - "48 shutdown\n", - rows.size()); + printf("kinds: %zu points at %zu leaf temperatures\n", rows.size(), + sizeof kExpectedKinds / sizeof kExpectedKinds[0]); + for (const TempKinds &e : kExpectedKinds) { + printf(" T = %4.1f C %3d interior, %2d pinned (%2d wet, %2d dry), " + "%2d shutdown\n", + e.leaf_temp, e.interior, e.pinned_wet + e.pinned_dry, e.pinned_wet, + e.pinned_dry, e.shutdown); + } } return failures == 0 ? 0 : 1; } const char *kHeader = - "psi_soil\tppfd\tvpd\tlayers\tpsi_stem\topt_root_psi\tci\tassim\ttranspiration\t" - "gc\tprofit\te_up\tuptake\n"; + "psi_soil\tppfd\tvpd\tleaf_temp\tlayers\tpsi_stem\topt_root_psi\tci\tassim\t" + "transpiration\tgc\tprofit\te_up\tuptake\n"; void write_row(FILE *f, const Row &r) { - fprintf(f, "%.17g\t%.17g\t%.17g\t%d", r.psi_soil, r.ppfd, r.vpd, r.layers); + fprintf(f, "%.17g\t%.17g\t%.17g\t%.17g\t%d", r.psi_soil, r.ppfd, r.vpd, + r.leaf_temp, r.layers); for (double v : {r.psi_stem, r.opt_root_psi, r.ci, r.assim, r.transpiration, r.gc, r.profit, r.e_up, r.uptake}) { fprintf(f, "\t%.17g", v); @@ -296,12 +346,14 @@ int compare(Tolerance tol) { break; } Row g{}; - // 4 inputs then 9 outputs + // 5 inputs then 9 outputs const int n = sscanf( - line, "%lg\t%lg\t%lg\t%d\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg", - &g.psi_soil, &g.ppfd, &g.vpd, &g.layers, &g.psi_stem, &g.opt_root_psi, &g.ci, - &g.assim, &g.transpiration, &g.gc, &g.profit, &g.e_up, &g.uptake); - if (n != 13) { + line, + "%lg\t%lg\t%lg\t%lg\t%d\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg\t%lg", + &g.psi_soil, &g.ppfd, &g.vpd, &g.leaf_temp, &g.layers, &g.psi_stem, + &g.opt_root_psi, &g.ci, &g.assim, &g.transpiration, &g.gc, &g.profit, + &g.e_up, &g.uptake); + if (n != 14) { fprintf(stderr, "FAIL: row %zu is malformed (%d fields)\n", i, n); ++failures; continue; @@ -345,10 +397,10 @@ int compare(Tolerance tol) { if (!ok) { if (failures < 20) { fprintf(stderr, - "FAIL psi_soil=%g ppfd=%g vpd=%g layers=%d %s: got %.17g, " + "FAIL psi_soil=%g ppfd=%g vpd=%g T=%g layers=%d %s: got %.17g, " "want %.17g (rel %.3g)\n", - r.psi_soil, r.ppfd, r.vpd, r.layers, fd.name, fd.got, fd.want, - rd); + r.psi_soil, r.ppfd, r.vpd, r.leaf_temp, r.layers, fd.name, + fd.got, fd.want, rd); } ++failures; } @@ -366,10 +418,11 @@ int compare(Tolerance tol) { char worst[256] = "none (bit-identical)"; if (worst_rel > 0.0) { snprintf(worst, sizeof worst, - "%.3g at psi_soil=%g ppfd=%g vpd=%g layers=%d %s " + "%.3g at psi_soil=%g ppfd=%g vpd=%g T=%g layers=%d %s " "(got %.17g, want %.17g)", worst_rel, worst_row.psi_soil, worst_row.ppfd, worst_row.vpd, - worst_row.layers, worst_desc, worst_got, worst_want); + worst_row.leaf_temp, worst_row.layers, worst_desc, worst_got, + worst_want); } const bool exact_mode = tol.argmax < 0.0; @@ -430,14 +483,20 @@ int compare(Tolerance tol) { // platform is NOT the fix -- it just moves the failure to the first one. // // The interesting part is the SIZE of the disagreement, because it is not one -// number. Measured over the full grid on Linux, the nine reported fields split -// into two classes three orders of magnitude apart: +// number. Read off this program's own summary line on Linux CI, the nine reported +// fields split into two classes five orders of magnitude apart, and gcc and clang +// agree exactly: // // gcc clang -// profit 1.85e-06 5.87e-07 +// profit 2.14e-09 2.14e-09 // psi_stem, collar, ci, assim, // transpiration, gc, e_up, -// uptake 5.53e-04 2.73e-04 +// uptake 1.4e-04 1.4e-04 +// +// ⚠️ NOTHING ASSERTS THAT BLOCK, so it rots in silence -- it has been wrong three +// times. **If you need a magnitude, read the summary line, not this comment and not +// the FAIL lines**: the failure list is truncated at 20 and biased toward whichever +// rows come first. // // That split is structural, not luck. `find_root_collar_psi` maximises profit // over the collar potential, and the maximum is FLAT: curvature k measured diff --git a/tests/cpp/test_leaf.cpp b/tests/cpp/test_leaf.cpp index c214f6b..e0c0dd7 100644 --- a/tests/cpp/test_leaf.cpp +++ b/tests/cpp/test_leaf.cpp @@ -61,6 +61,10 @@ struct Drivers { double area_leaf = 0.05; }; +// set_traits' fourteenth argument, R_d_25: dark respiration at 25 C. The class +// default, so a call that is not about respiration can pass it and change nothing. +const double kRd25 = 1.44; + phylloptim::Leaf make_leaf(const Drivers &d, std::vector psi_soil, std::vector soil_depth) { phylloptim::Leaf l; @@ -773,7 +777,7 @@ void test_collar_solve_handles_a_pinned_optimum() { // bit-identical golden run says nothing here. The sequence below alternates kinds // on purpose, so an unwritten tag reads as the step before it. // -// The count check over the whole 288-point grid lives in test_golden.cpp; this is +// The count check over the whole golden grid lives in test_golden.cpp; this is // the other half -- that every path writes, and that the tag comes from the // branch rather than from the numbers. void test_operating_point_kind_is_written_by_every_path() { @@ -857,7 +861,8 @@ void test_operating_point_kind_is_written_by_every_path() { // classification is part of that state (hazard 10 / setup_clean_leaf). l.set_traits(l.vcmax_25, l.stem_c, l.stem_b, l.psi_crit, l.roots_.root_c, l.roots_.root_b, l.roots_.root_psi_crit, l.beta2, l.jmax_25, l.a, - l.curv_fact_elec_trans, l.curv_fact_colim, l.cost_scale_TF24); + l.curv_fact_elec_trans, l.curv_fact_colim, l.cost_scale_TF24, + l.R_d_25); ok(l.operating_point_kind() == Kind::Unsolved, "set_traits clears the classification with the rest of the solved state"); @@ -2002,7 +2007,7 @@ void test_temperature_parameters_are_settable() { ok(base.vcmax_ha_ == phylloptim::vcmax_ha, "vcmax_ha_ defaults to the constant"); ok(base.jmax_d_S_ == phylloptim::jmax_d_S, "jmax_d_S_ defaults to the constant"); ok(base.gamma_25_ == phylloptim::gamma_25, "gamma_25_ defaults to the constant"); - near(base.rd_to_vcmax_ratio_, 0.015, 1e-12, "rd_to_vcmax_ratio_ default"); + near(base.R_d_25, 1.44, 1e-12, "R_d_25 default"); // Raising the Vcmax activation energy raises Vcmax above the 25 C reference, // so a 25 C leaf should be unaffected but a warm one should assimilate more. @@ -2017,14 +2022,13 @@ void test_temperature_parameters_are_settable() { "a larger activation energy gives a larger vcmax at 35 C"); } - // Respiration fraction: doubling it must lower assimilation. + // Respiration: doubling it must lower assimilation. { phylloptim::Leaf r2 = make_leaf(d, {2.0}, {1.0}); - r2.rd_to_vcmax_ratio_ = 0.030; + r2.R_d_25 = 2.0 * r2.R_d_25; r2.update_temperature_dependent_params(d.leaf_temp); r2.find_root_collar_psi(); - ok(r2.assim_colimited_ < A_base, - "doubling the respiration fraction lowers assimilation"); + ok(r2.assim_colimited_ < A_base, "doubling R_d_25 lowers assimilation"); ok(r2.R_d_ > base.R_d_, "and raises R_d"); } @@ -2039,6 +2043,204 @@ void test_temperature_parameters_are_settable() { } } +// ⚠️ THE ASSERTIONS ABOVE ALL PUSH THEIR CHANGE THROUGH BY CALLING +// update_temperature_dependent_params() DIRECTLY, AND THAT IS WHY THEY PASSED +// WHILE THE FEATURE WAS BROKEN FROM R. A caller does not have that route: they set +// the field and then set the drivers, which is the one path that took a cache hit +// and silently kept the old response. The test worked around the bug it should +// have caught. +// +// So this asserts the REALISTIC path, twice over: setting a temperature-response +// parameter on an already-solved leaf and re-supplying the SAME drivers must change +// the answer, and must land on exactly what a freshly constructed leaf gives. +// +// Bit-exactness is the right bar for the second half -- the two routes share no +// code, so anything the cache fails to invalidate shows up as a difference. #41. +void test_temperature_params_invalidate_cache() { + printf("setting a temperature parameter invalidates the cache\n"); + Drivers d; + + // The realistic route: solve, change the parameter, re-supply the same drivers. + phylloptim::Leaf warm = make_leaf(d, {2.0}, {1.0}); + warm.find_root_collar_psi(); + const double A_before = warm.assim_colimited_; + const double Rd_before = warm.R_d_; + + warm.R_d_25 = 2.0 * warm.R_d_25; + warm.set_physiology(fixture::root_network({1.0 / d.area_leaf}, {1.0}), d.PPFD, + {2.0}, {1.0}, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, + d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); + warm.find_root_collar_psi(); + + ok(warm.R_d_ != Rd_before, + "re-supplying the same drivers after a parameter change recomputes R_d"); + ok(warm.assim_colimited_ != A_before, + "and the operating point moves"); + near(warm.R_d_, 2.0 * Rd_before, 1e-12, + "doubling R_d_25 doubles R_d at the same temperature"); + + // And it must agree bit-for-bit with never having had the stale value. + phylloptim::Leaf fresh = make_leaf(d, {2.0}, {1.0}); + fresh.R_d_25 = 2.0 * fresh.R_d_25; + fresh.set_physiology(fixture::root_network({1.0 / d.area_leaf}, {1.0}), d.PPFD, + {2.0}, {1.0}, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, + d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); + fresh.find_root_collar_psi(); + ok(warm.assim_colimited_ == fresh.assim_colimited_, + "a re-parameterised leaf is bit-identical to one built with the value"); + ok(warm.R_d_ == fresh.R_d_, "R_d likewise"); + + // ⚠️ The same hole covered vcmax_25, which is a TRAIT. set_traits() remains the + // correct way to change one -- the vulnerability splines and the solved point + // need clearing too -- but the silent-wrong-number half of hazard 10 is gone. + phylloptim::Leaf vc = make_leaf(d, {2.0}, {1.0}); + vc.find_root_collar_psi(); + const double vcmax_before = vc.vcmax_; + vc.vcmax_25 = vc.vcmax_25 * 1.5; + vc.set_physiology(fixture::root_network({1.0 / d.area_leaf}, {1.0}), d.PPFD, + {2.0}, {1.0}, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, + d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); + ok(vc.vcmax_ > vcmax_before, + "a bare vcmax_25 write no longer leaves vcmax_ describing the old value"); + + // The cache must still BE a cache: identical inputs twice must not recompute + // into a different answer. + phylloptim::Leaf same = make_leaf(d, {2.0}, {1.0}); + same.find_root_collar_psi(); + const double A_once = same.assim_colimited_; + same.set_physiology(fixture::root_network({1.0 / d.area_leaf}, {1.0}), d.PPFD, + {2.0}, {1.0}, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, + d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); + same.find_root_collar_psi(); + ok(same.assim_colimited_ == A_once, + "unchanged inputs still give a bit-identical answer"); +} + +// R_d's TEMPERATURE RESPONSE (#41). +// +// ⚠️ THE GOLDEN FILE IS NEARLY BLIND TO THIS, and that is the reason this test +// exists. Every reference value in the model is DEFINED at 25 C, so a change to any +// response curve is inert there by construction; the golden grid carries one hot +// block for exactly this reason, and this test is what pins the response itself. +void test_rd_temperature_response() { + printf("R_d rises with temperature\n"); + Drivers d; + + // R_d IS R_d_25 at the reference, exactly. The trait is the value there, not a + // scale on anything. + { + phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); + near(l.R_d_, l.R_d_25, 1e-12, "R_d at 25 C is R_d_25"); + } + + // The direction: R_d must RISE, including above Vcmax's thermal optimum near + // 31 C, so 45 C is comfortably past it. + double rd_prev = -1.0; + for (double T : {25.0, 35.0, 45.0}) { + phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); + l.update_temperature_dependent_params(T); + ok(l.R_d_ > rd_prev, "R_d rises with temperature"); + rd_prev = l.R_d_; + } + + // Tjoelker semantics. Q10 is evaluated at the MEAN of T and the reference, so a + // 10 K rise from 25 C multiplies R_d by Q10(30) = 3.09 - 0.043*30 = 1.80 -- not + // by the 2.015 that Q10(25) would give. Checking the number rather than just the + // direction is what distinguishes this from a constant Q10. + { + phylloptim::Leaf a = make_leaf(d, {2.0}, {1.0}); + phylloptim::Leaf b = make_leaf(d, {2.0}, {1.0}); + a.update_temperature_dependent_params(25.0); + b.update_temperature_dependent_params(35.0); + const double q10_at_30 = 3.09 - 0.0430 * 30.0; + near(b.R_d_, q10_at_30 * a.R_d_, 1e-12, + "a 10 K rise scales R_d by Q10 at the midpoint temperature"); + ok(q10_at_30 < 2.0, "and that Q10 is below 2, i.e. the decline is active"); + } + + // A constant Q10 must stay reachable: slope zero, intercept the value. + { + phylloptim::Leaf a = make_leaf(d, {2.0}, {1.0}); + phylloptim::Leaf b = make_leaf(d, {2.0}, {1.0}); + a.rd_q10_intercept_ = 2.0; a.rd_q10_slope_ = 0.0; + b.rd_q10_intercept_ = 2.0; b.rd_q10_slope_ = 0.0; + a.update_temperature_dependent_params(25.0); + b.update_temperature_dependent_params(35.0); + near(b.R_d_, 2.0 * a.R_d_, 1e-12, + "slope zero recovers a constant Q10 exactly"); + } + + // A measured value is used verbatim, and is INDEPENDENT of vcmax_25 -- R_d_25 is + // a trait in its own right, not a fraction of Vcmax. + { + phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); + l.R_d_25 = 0.525; // Sabot's Rlref, as measured + l.update_temperature_dependent_params(25.0); + near(l.R_d_, 0.525, 1e-12, "a set R_d_25 is used verbatim at 25 C"); + l.vcmax_25 = 2.0 * l.vcmax_25; + l.update_temperature_dependent_params(25.0); + near(l.R_d_, 0.525, 1e-12, "and does not follow vcmax_25"); + } + + // An unset or negative R_d_25 FAILS rather than falling back to a derivation. + for (double bad : {std::numeric_limits::quiet_NaN(), -1.0}) { + phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); + l.R_d_25 = bad; + bool threw = false; + try { + l.update_temperature_dependent_params(30.0); + } catch (const std::runtime_error &) { + threw = true; + } + ok(threw, "an unusable R_d_25 is refused, not worked around"); + } + + // The response, and the LIMIT it makes reachable, printed rather than asserted + // cell by cell: a higher R_d can drive net assimilation negative across the whole + // [gamma*, ca] bracket, and then there is no supply == demand root at all. At the + // defaults that happens by 45 C, which is a number a caller needs. + printf(" R_d and assimilation against leaf temperature:\n"); + for (double T : {15.0, 25.0, 35.0, 40.0, 45.0}) { + phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); + l.update_temperature_dependent_params(T); + l.find_root_collar_psi(); + printf(" T = %4.1f C R_d %6.3f A %8.4f%s\n", T, l.R_d_, + l.assim_colimited_, + l.ci_at_compensation_point_ ? " <-- shut down" : ""); + } + + // ⚠️ AND IT MUST SHUT DOWN RATHER THAN THROW. A leaf too hot to gain carbon at + // any internal CO2 is a physical state, not a solver failure -- the energy-balance + // path always treated it that way and the prescribed-temperature path used to + // throw, which was only invisible while R_d was too small to get there. + { + phylloptim::Leaf hot = make_leaf(d, {2.0}, {1.0}); + bool threw = false; + try { + hot.update_temperature_dependent_params(45.0); + hot.find_root_collar_psi(); + } catch (const std::exception &) { + threw = true; + } + ok(!threw, "a leaf too hot to gain carbon shuts down instead of throwing"); + ok(hot.ci_at_compensation_point_, + "and says so, rather than reporting an ordinary operating point"); + near(hot.ci_, hot.gamma_ * hot.umol_per_mol_to_Pa_, 1e-12, + "ci sits at the compensation point"); + ok(hot.assim_colimited_ <= 0.0, "with no net carbon gain"); + } + + // ⚠️ A GENUINE solver failure must STILL throw -- the point of not simply + // deleting the gate. An unsatisfiable bracket where the root IS inside it (here + // forced by a non-finite target via a poisoned ca) is a bug, not a hot leaf. + { + phylloptim::Leaf ok_leaf = make_leaf(d, {2.0}, {1.0}); + ok_leaf.find_root_collar_psi(); + ok(!ok_leaf.ci_at_compensation_point_, + "an ordinary leaf is not flagged as shut down"); + } +} + // set_traits exists so a gradient loop can perturb a trait without rebuilding the // object. That is only worth having if re-traiting is INDISTINGUISHABLE from // constructing afresh, so that is what is asserted -- bit-exactly, which is a @@ -2088,7 +2290,7 @@ void test_perturb_stem_b_matches_a_rebuild() { phylloptim::Leaf rebuilt = make_leaf(d, {2.0}, {1.0}); rebuilt.find_root_collar_psi(); rebuilt.set_traits(96.0, 2.680147, b_new, 5.870283, 2.680147, 3.898245, - 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5); + 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, kRd25); rebuilt.set_physiology(fixture::root_network(mrp, depth), d.PPFD, psi_soil, depth, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); @@ -2121,7 +2323,7 @@ void test_perturb_stem_b_matches_a_rebuild() { phylloptim::Leaf fresh = make_leaf(d, {2.0}, {1.0}); fresh.find_root_collar_psi(); rescaled.set_traits(96.0, 2.680147, 3.898245, 5.870283, 2.680147, 3.898245, - 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5); + 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, kRd25); rescaled.set_physiology(fixture::root_network(mrp, depth), d.PPFD, psi_soil, depth, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); @@ -2170,7 +2372,7 @@ void test_set_traits_matches_a_fresh_leaf() { phylloptim::Leaf reused = make_leaf(d, {2.0}, {1.0}); reused.find_root_collar_psi(); reused.set_traits(t[0], t[1], t[2], t[3], t[4], t[5], t[6], t[7], t[8], t[9], - t[10], t[11], t[12]); + t[10], t[11], t[12], kRd25); reused.set_physiology(fixture::root_network(mrp, depth), d.PPFD, psi_soil, depth, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); reused.find_root_collar_psi(); @@ -2200,7 +2402,7 @@ void test_set_traits_matches_a_fresh_leaf() { phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); const double vcmax_before = l.vcmax_; l.set_traits(96.0 * 2.0, 2.680147, 3.898245, 5.870283, 2.680147, 3.898245, - 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5); + 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, kRd25); std::vector mrp{1.0 / d.area_leaf}, psi_soil{2.0}, depth{1.0}; // The SAME leaf_temp and atm_o2_kpa, which is what arms the cache. l.set_physiology(fixture::root_network(mrp, depth), d.PPFD, psi_soil, depth, d.K_s * d.theta / d.h, @@ -2217,7 +2419,7 @@ void test_set_traits_matches_a_fresh_leaf() { phylloptim::Leaf l = make_leaf(d, {2.0}, {1.0}); const double E_before = l.transpiration(3.0, 1.0); l.set_traits(96.0, 2.680147, 3.898245 * 1.5, 5.870283, 2.680147, 3.898245, - 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5); + 5.870283, 1.5, 157.44, 0.30, 0.7, 0.99, 7.5, kRd25); std::vector mrp{1.0 / d.area_leaf}, psi_soil{2.0}, depth{1.0}; l.set_physiology(fixture::root_network(mrp, depth), d.PPFD, psi_soil, depth, d.K_s * d.theta / d.h, d.atm_vpd, d.ca, d.leaf_temp, d.atm_o2_kpa, d.atm_kpa); @@ -2245,7 +2447,7 @@ void test_set_traits_matches_a_fresh_leaf() { bool threw = false; try { l.set_traits(t[0], t[1], t[2], t[3], t[4], t[5], t[6], t[7], t[8], t[9], - t[10], t[11], t[12]); + t[10], t[11], t[12], kRd25); } catch (const std::runtime_error &) { threw = true; } @@ -2417,6 +2619,8 @@ int main() { test_leaf_on_single_potential(); test_root_network_from_carbon(); test_temperature_parameters_are_settable(); + test_temperature_params_invalidate_cache(); + test_rd_temperature_response(); test_set_traits_matches_a_fresh_leaf(); test_perturb_stem_b_matches_a_rebuild(); test_bad_input_throws(); diff --git a/tests/testthat/gradient_golden.tsv b/tests/testthat/gradient_golden.tsv index ba54790..bc5db9d 100644 --- a/tests/testthat/gradient_golden.tsv +++ b/tests/testthat/gradient_golden.tsv @@ -1,16 +1,21 @@ case status method par A gc psi_stem collar -interior-1layer interior ift vcmax_25 0x1.19f24c79f383p-6 0x1.3259b788b7cd8p-15 0x1.06a759124089ep-8 0x1.c9aa56f8160ap-10 +interior-1layer interior ift vcmax_25 0x1.56ff4d6eecf96p-6 0x1.6279997564ff5p-15 0x1.2fe9f734f59d8p-8 0x1.08c7ad051fb7dp-9 interior-1layer interior ift stem_b 0x1.6c5b48adf2fp+1 0x1.7ab19a189bb21p-7 0x1.d9c2457829579p-1 0x1.1add81b8d5d2fp-1 interior-1layer interior ift psi_crit 0x0p+0 0x0p+0 0x0p+0 0x0p+0 -interior-5layer interior ift vcmax_25 0x1.562cd013972cdp-5 0x1.1f2719b2a9b2p-17 0x1.7b34095a49116p-12 0x1.d034f56d422fcp-13 +interior-1layer interior ift R_d_25 -0x1.fd6a09155bf1cp-3 -0x1.90ddd402a632ep-12 -0x1.57b035f654ff8p-5 -0x1.2b6ec9ddabc73p-6 +interior-5layer interior ift vcmax_25 0x1.a789fd22240c2p-5 0x1.f668e2d6ae349p-16 0x1.4bbb591c8bbecp-10 0x1.9618142da1224p-11 interior-5layer interior ift stem_b 0x1.bf615f57bdaf1p+0 0x1.40cec78217423p-6 0x1.35865423734e6p-1 0x1.03506a09d13edp-1 interior-5layer interior ift psi_crit 0x0p+0 0x0p+0 0x0p+0 0x0p+0 -pinned-dry-3layer pinned fd vcmax_25 0x1.d65f7a06148aap-7 0x0p+0 0x0p+0 0x0p+0 +interior-5layer interior ift R_d_25 -0x1.53043af91afd9p-1 -0x1.75c8e3e4fefbp-10 -0x1.ed9b3452956e1p-5 -0x1.2e209f7e6b335p-5 +pinned-dry-3layer pinned fd vcmax_25 0x1.1f8090c0306p-6 0x0p+0 0x0p+0 0x0p+0 pinned-dry-3layer pinned fd stem_b 0x1.2ccb4ca42ff14p+2 0x1.64b64bdad4946p-6 0x1.33ff011ff4998p-14 0x1.c3ef65a37fee1p-2 pinned-dry-3layer pinned fd psi_crit 0x1.41dade66b0dcp+0 0x1.7db02a11ba0cbp-8 0x1.fff9995bb6188p-1 0x1.e3a34a2bcbb21p-4 -shutdown-1layer no-gradient fd vcmax_25 -0x1.eb851eb7cb5p-7 0x0p+0 0x0p+0 0x0p+0 +pinned-dry-3layer pinned fd R_d_25 -0x1.b3f6e43dfed39p-3 0x0p+0 0x0p+0 0x0p+0 +shutdown-1layer no-gradient fd vcmax_25 0x0p+0 0x0p+0 0x0p+0 0x0p+0 shutdown-1layer no-gradient fd stem_b 0x0p+0 0x0p+0 0x0p+0 0x0p+0 shutdown-1layer no-gradient fd psi_crit 0x0p+0 0x0p+0 0x1.000000001aa4dp+0 0x1.000000001aa4dp+0 -single-potential interior ift vcmax_25 0x1.1e8d0cc6a7624p-12 0x1.46b9a3f216e9ap-21 0x1.c5e7ef6149ddep-13 0x1.a4ed700e9cb7ep-13 +shutdown-1layer no-gradient fd R_d_25 -0x1.ffffffff73c8bp-1 0x0p+0 0x0p+0 0x0p+0 +single-potential interior ift vcmax_25 0x1.8dbb95a5a7daap-11 0x1.8665f5c42e12fp-20 0x1.0f2ea755b7941p-11 0x1.f6f5831d8118cp-12 single-potential interior ift leaf_specific_conductance_max 0x1.61e2e05d142cfp+11 0x1.116a882643229p+3 0x1.c7141229c1e05p+10 0x1.603f57174c2c4p+11 single-potential interior ift resistance -0x1.f8de9025064bep-14 -0x1.861138fe7344ap-22 -0x1.34162dac5854ep-14 -0x1.0ed249f513811p-14 +single-potential interior ift R_d_25 -0x1.090f44c09b126p-5 -0x1.d8fdb4470b455p-15 -0x1.488db9f00ccp-6 -0x1.30aebd98fd4a3p-6 diff --git a/tests/testthat/helper-golden.R b/tests/testthat/helper-golden.R index de1e96b..204fb8b 100644 --- a/tests/testthat/helper-golden.R +++ b/tests/testthat/helper-golden.R @@ -39,15 +39,39 @@ golden_tolerance <- function(field) { if (identical(field, "profit")) 1.0e-5 else 1.0e-3 } +# ⚠️ THE RECORDED GRADIENTS NEED THEIR OWN, LOOSER TOLERANCE, and borrowing the one +# above was wrong -- it just happened not to fail until #41 added a column. +# +# A gradient here is a FINITE DIFFERENCE of the solve, so cross-platform it carries +# the solve's own ~1e-9 floor DIVIDED BY THE STEP. The step is RELATIVE, so the +# amplification is set by the differentiated parameter's own magnitude, and the +# smallest parameter in the file decides the tolerance for all of it. +# +# Measured on Linux CI: `dA/dR_d_25` at interior-1layer disagrees by 1.3e-03 +# relative, against 1.3e-04 for every column that was here before. `R_d_25` is 1.44 +# where `vcmax_25` is 96 -- a 67x smaller absolute step at the same relative one -- +# and the arithmetic closes: 1.3e-03 x 0.2487 x 2h = 9.3e-10, i.e. the floor itself. +# +# Confirmed independently by the step sweep: at `step = 1e-7` the `R_d_25` column has +# already moved 1.3% while `vcmax_25` has moved 0.2%. That column goes +# noise-dominated first, and it is the one that sets this number. +# +# 5e-03 leaves ~4x headroom over the one observation there is. It cannot hide a real +# change: #41's own reallocation moved these cells by 16% to 250%, two orders above +# this. ⚠️ It IS one CI observation, so read the worst-difference line the test +# prints on every run rather than assuming the headroom is still there. +gradient_golden_tolerance <- function() 5.0e-3 + # expect_identical where it can hold, expect_equal with the measured per-field # tolerance where it cannot. Wrapped in one place so no individual test has to # decide, and so the reason lives next to the policy rather than at every call. -expect_golden <- function(actual, expected_hex, field, label) { +expect_golden <- function(actual, expected_hex, field, label, + tolerance = golden_tolerance(field)) { expected <- as.numeric(expected_hex) if (golden_bit_exact_platform()) { expect_identical(actual, expected, label = paste(label, field)) } else { - expect_equal(actual, expected, tolerance = golden_tolerance(field), + expect_equal(actual, expected, tolerance = tolerance, label = paste(label, field)) } } diff --git a/tests/testthat/test-gradient-batch.R b/tests/testthat/test-gradient-batch.R index 06508b6..c421d7a 100644 --- a/tests/testthat/test-gradient-batch.R +++ b/tests/testthat/test-gradient-batch.R @@ -85,9 +85,9 @@ test_that("the parameter enumeration is the same order in R and in C++", { "resistance") expect_identical(gradient_par_names(), r_side) # And the count, which is what a positional trait call would silently break: - # thirteen traits then the two that are not traits. - expect_length(gradient_par_names(), 15L) - expect_identical(gradient_par_names()[1:13], names(leaf_traits())) + # fourteen traits then the two that are not traits. + expect_length(gradient_par_names(), 16L) + expect_identical(gradient_par_names()[1:14], names(leaf_traits())) }) test_that("the batch reproduces leaf_gradient() bit-for-bit across the grid", { @@ -187,21 +187,21 @@ test_that("the recorded gradients have not moved", { # back one ULP out (#13). gold <- utils::read.delim(test_path("gradient_golden.tsv"), stringsAsFactors = FALSE) + pars_grid <- c("vcmax_25", "stem_b", "psi_crit", "R_d_25") cases <- list( - "interior-1layer" = list(args = batch_drivers(2.0), - pars = c("vcmax_25", "stem_b", "psi_crit")), + "interior-1layer" = list(args = batch_drivers(2.0), pars = pars_grid), "interior-5layer" = list(args = batch_drivers(0.5, vpd = 0.5, layers = 5L), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = pars_grid), "pinned-dry-3layer" = list(args = batch_drivers(4.0, vpd = 0.5, layers = 3L), - pars = c("vcmax_25", "stem_b", "psi_crit")), - "shutdown-1layer" = list(args = batch_drivers(6.0), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = pars_grid), + "shutdown-1layer" = list(args = batch_drivers(6.0), pars = pars_grid), "single-potential" = list( args = list(psi_soil = 1.5, PPFD = 900, atm_vpd = 2.0, supply = leaf_supply_single(), root_network = series_resistance(1e4)), - pars = c("vcmax_25", "leaf_specific_conductance_max", "resistance"))) + pars = c("vcmax_25", "leaf_specific_conductance_max", "resistance", + "R_d_25"))) expect_setequal(unique(gold$case), names(cases)) # ⚠️ BIT-EXACT ONLY ON THE PLATFORM THAT GENERATED IT, macOS/arm64, exactly as @@ -210,12 +210,10 @@ test_that("the recorded gradients have not moved", { # test-golden.R's first version made. libm's exp/pow are not bit-reproducible # between glibc on x86-64 and Apple's libm on arm64. # - # THE TOLERANCE IS NOT A GUESS AND NOT NEW. These are derivatives of outputs - # evaluated at the ARGMAX of a flat maximum, so they belong to the golden file's - # own sqrt-amplified class -- and `golden_tolerance()` is that policy, reused - # here rather than restated. Measured worst relative disagreement on Linux is - # 1.3e-4, against the golden file's 1.4e-4 for the same class: a central - # difference cancels the systematic part of a libm difference but not all of it. + # THE TOLERANCE IS `gradient_golden_tolerance()`, not the solved-output one: a + # gradient here is a finite difference, so it carries the solve's floor divided by + # the step, and the smallest-magnitude parameter sets it for the whole file. See + # that function for the arithmetic. # # ⚠️ Read the SUMMARY LINE below for a magnitude, never the FAIL lines. The # figures in this package's guide were wrong twice because a truncated failure @@ -232,7 +230,8 @@ test_that("the recorded gradients have not moved", { for (out in c("A", "gc", "psi_stem", "collar")) { got <- g$gradient[1, rows$par[[i]], out] expect_golden(got, rows[[out]][[i]], out, - paste(nm, rows$par[[i]])) + paste(nm, rows$par[[i]]), + tolerance = gradient_golden_tolerance()) ref <- as.numeric(rows[[out]][[i]]) if (ref != 0) { worst <- max(worst, abs(got - ref) / abs(ref)) @@ -333,8 +332,8 @@ test_that("per-observation theta differentiates each row at its own parameters", b <- leaf_batch(psi_soil = psv, PPFD = 900) theta <- t(vapply(traits, function(tr) { - unname(c(unlist(tr)[gradient_par_names()[1:13]], 3.14e-5, NA_real_)) - }, numeric(15))) + unname(c(unlist(tr)[gradient_par_names()[1:14]], 3.14e-5, NA_real_)) + }, numeric(16))) g <- leaf_gradient_batch(b, theta = theta, pars = pars) for (i in seq_along(psv)) { @@ -451,8 +450,8 @@ test_that("`pars` order does not change any gradient (#72)", { # ⚠️ And the predecessor that made the defect WORST, which is not the one you # would pick by eye: `a` = 0.30 and `curv_fact_colim` = 0.99 take the absolute # 1e-6 step floor rather than a relative step, and `stem_c`'s perturbation - # REBUILDS the very curve the `stem_b` shortcut then rescales. Each of the - # thirteen is checked as a predecessor rather than a sample of them. + # REBUILDS the very curve the `stem_b` shortcut then rescales. Every trait is + # checked as a predecessor rather than a sample of them. solo <- leaf_gradient_batch(b, pars = "stem_b")$gradient[1, "stem_b", ] for (p in setdiff(names(leaf_traits()), "stem_b")) { got <- leaf_gradient_batch(b, pars = c(p, "stem_b"))$gradient[1, "stem_b", ] @@ -510,11 +509,11 @@ test_that("leaf_gradient_batch() rejects what it cannot do", { # `traits` and `theta` both say where the gradient is taken, so passing both is # refused rather than resolved in favour of one of them. - th <- matrix(1, nrow = 1, ncol = 15) + th <- matrix(1, nrow = 1, ncol = 16) expect_error(leaf_gradient_batch(b, traits = leaf_traits(), theta = th), "pass one") - expect_error(leaf_gradient_batch(b, theta = matrix(1, 1, 14)), "15 columns") - expect_error(leaf_gradient_batch(b, theta = matrix(1, 3, 15)), + expect_error(leaf_gradient_batch(b, theta = matrix(1, 1, 15)), "16 columns") + expect_error(leaf_gradient_batch(b, theta = matrix(1, 3, 16)), "1 row or one per observation") expect_error(leaf_gradient_batch(b, theta = as.data.frame(th)), "numeric matrix") diff --git a/tests/testthat/test-gradient.R b/tests/testthat/test-gradient.R index 7b5d264..440a01e 100644 --- a/tests/testthat/test-gradient.R +++ b/tests/testthat/test-gradient.R @@ -167,10 +167,17 @@ test_that("a pinned optimum takes the fallback, and the composite would be wrong # a factor of 1.6 out for vcmax_25 there rather than seven orders, so a test # that only looked at the wet rows would let a threshold drift past it. dry <- grid_gradient(4, vpd = 0.5, layers = 3L, - pars = c("stem_b", "vcmax_25")) + pars = c("stem_b", "vcmax_25", "R_d_25")) expect_identical(dry$status, "pinned") - expect_equal(dry$gradient["vcmax_25", "A"], 0.014357, tolerance = 1e-3) + expect_equal(dry$gradient["vcmax_25", "A"], 0.017548, tolerance = 1e-3) expect_equal(dry$gradient["stem_b", "A"], 4.6991, tolerance = 1e-3) + + # `dA/dvcmax_25` is a PARTIAL at fixed respiration, since `R_d_25` is its own + # trait. A fit that wants respiration to follow Vcmax adds the two columns, so + # that combination is asserted rather than left implicit. + expect_equal(dry$gradient["vcmax_25", "A"] + + 0.015 * dry$gradient["R_d_25", "A"], + 0.014357, tolerance = 1e-3) }) test_that("at a pinned optimum the BOUND's own trait carries the gradient", { @@ -206,12 +213,19 @@ test_that("a shut-down operating point reports no gradient and still differences # psi_soil = 6 is drier than psi_crit, so there is no optimisation to # differentiate: dprofit returns a sentinel zero rather than a derivative, and # H comes back zero with it. The composite has nothing to stand on and says so - # -- but the gradient itself is not zero, because R_d still depends on - # vcmax_25, so the fallback still has work to do. - g <- grid_gradient(6.0, pars = c("vcmax_25", "stem_b")) + # -- but the gradient itself is not all zero, because a shut-down leaf still + # respires, so the fallback still has work to do. + # + # WHICH parameter carries it is the sharpest statement in the suite: `A = -R_d` + # exactly here, so `dA/dR_d_25` is -1 and `dA/dvcmax_25` is EXACTLY zero -- + # vcmax_25 does not reach A at all at a shut-down point, so both perturbed solves + # return the same bits. The -1 is a central difference and lands within ~6e-11. + g <- grid_gradient(6.0, pars = c("vcmax_25", "stem_b", "R_d_25")) expect_identical(g$status, "no-gradient") expect_identical(g$method, "fd") - expect_equal(g$gradient["vcmax_25", "A"], -0.015, tolerance = 1e-4) + expect_equal(g$value[["A"]], -leaf_traits()$R_d_25) + expect_equal(g$gradient["R_d_25", "A"], -1, tolerance = 1e-8) + expect_identical(g$gradient["vcmax_25", "A"], 0) expect_equal(g$gradient["stem_b", "A"], 0) # Forcing the composite here is an error rather than a wrong number: unlike a @@ -590,11 +604,12 @@ test_that("leaf_gradient() refuses the combinations that would disagree", { test_that("the setter's positional trait call cannot drift in arity", { # `.gradient_setter()` applies traits POSITIONALLY, straight onto the object, to - # skip rebuilding a leaf_traits per perturbation. That is a hard-coded thirteen. If + # skip rebuilding a leaf_traits per perturbation. That is a hard-coded FOURTEEN. If # a trait is added to leaf_traits() and to the C++ setter, nothing about that call # fails to compile -- it would silently pass the wrong value for every argument # after the new one. So the arity is asserted here rather than trusted. - expect_length(leaf_traits(), 13L) - expect_length(formals(leaf_model()$set_traits), 13L) + # + expect_length(leaf_traits(), 14L) + expect_length(formals(leaf_model()$set_traits), 14L) expect_identical(names(leaf_traits()), names(formals(leaf_model()$set_traits))) }) diff --git a/tests/testthat/test-surface.R b/tests/testthat/test-surface.R index 8f49bd3..2f432e4 100644 --- a/tests/testthat/test-surface.R +++ b/tests/testthat/test-surface.R @@ -17,8 +17,11 @@ test_that("leaf_traits() and leaf_control() partition the C++ constructor", { covered <- c(names(leaf_traits()), names(leaf_control())) expect_setequal(setdiff(ctor_args, covered), character(0)) + # `R_d_25` is a trait the constructor does not take: plant's own RcppR6 bindings + # pin this constructor by arity, so `leaf_model()` assigns the field afterwards. + # The test below checks that assignment really happens. expect_setequal(setdiff(covered, ctor_args), - c("integration_rule", "integration_tol")) + c("R_d_25", "integration_rule", "integration_tol")) expect_length(intersect(names(leaf_traits()), names(leaf_control())), 0) # And the split is the one the issue asked for: tolerances on the control @@ -59,6 +62,23 @@ test_that("a non-default trait reaches the model through leaf_model()", { brittle <- leaf_model(leaf_traits(stem_b = 2.0)) expect_lt(brittle$proportion_of_conductivity(2.0), leaf_model()$proportion_of_conductivity(2.0)) + + # ⚠️ `R_d_25` NEEDS ITS OWN CASE, because it is the one trait the constructor does + # not take: if `leaf_model()`'s assignment went away, every test above would still + # pass while `leaf_traits(R_d_25 = )` was accepted and silently ignored. + default_rd <- leaf_traits()$R_d_25 + expect_identical( + leaf_solve(psi_soil = 2.0, PPFD = 900, + traits = leaf_traits(R_d_25 = default_rd))$A, + base$A) + expect_lt(leaf_solve(psi_soil = 2.0, PPFD = 900, + traits = leaf_traits(R_d_25 = 2 * default_rd))$A, + base$A) + expect_gt(leaf_solve(psi_soil = 2.0, PPFD = 900, + traits = leaf_traits(R_d_25 = 0))$A, + base$A) + expect_error(leaf_traits(R_d_25 = -1), "non-negative") + expect_error(leaf_traits(R_d_25 = NA_real_), "finite") }) test_that("a control setting reaches the model and is not treated as a trait", { diff --git a/tests/testthat/test-temperature-response.R b/tests/testthat/test-temperature-response.R index 6ffbc94..993a5a5 100644 --- a/tests/testthat/test-temperature-response.R +++ b/tests/testthat/test-temperature-response.R @@ -1,6 +1,6 @@ # The temperature-response parameters, now reachable from R. # -# WHY THIS FILE EXISTS. These thirteen were public C++ members with no entry in +# WHY THIS FILE EXISTS. These fifteen were public C++ members with no entry in # inst/RcppR6_classes.yml, so from R the SHAPE of the temperature response was # fixed and unreachable. The eight derived quantities (vcmax_, jmax_, gamma_, # ko_, kc_, km_, R_d_, electron_transport_) were bound and settable, which made @@ -22,7 +22,9 @@ test_that("the temperature-response parameters are readable at their defaults", expect_equal(l$jmax_ha_, 30000) expect_equal(l$jmax_H_d_, 200000) expect_equal(l$jmax_d_S_, 650) - expect_equal(l$rd_to_vcmax_ratio_, 0.015) + expect_equal(l$R_d_25, 1.44) + expect_equal(l$rd_q10_intercept_, 3.09) + expect_equal(l$rd_q10_slope_, 0.0430) for (f in c("gamma_25_", "gamma_ha_", "kc_25_", "kc_ha_", "ko_25_", "ko_ha_")) { expect_true(is.finite(l[[f]]), info = f) @@ -76,23 +78,24 @@ test_that("changing a temperature parameter changes the solve, via set_traits", expect_gt(moved, base) }) -test_that("rd_to_vcmax_ratio_ reaches the solve", { +test_that("R_d_25 reaches the solve, and rises with temperature", { tr <- leaf_traits() - drive <- function(ratio) { - l <- leaf_model(traits = tr, control = leaf_control(), - supply = leaf_supply_single()) - if (!is.null(ratio)) l$rd_to_vcmax_ratio_ <- ratio - set_traits(l, tr) + drive <- function(rd_25, temp = 25) { + l <- leaf_model(traits = leaf_traits(R_d_25 = rd_25), + control = leaf_control(), supply = leaf_supply_single()) set_drivers(l, psi_soil = 0.5, PPFD = 1200, root_network = series_resistance(50), leaf_specific_conductance_max = 1e-4, atm_vpd = 1.0, ca = 40, - leaf_temp = 25, atm_o2_kpa = 20.9, atm_kpa = 101.325) + leaf_temp = temp, atm_o2_kpa = 20.9, atm_kpa = 101.325) l$find_root_collar_psi() - l$assim_colimited_ + c(A = l$assim_colimited_, R_d = l$R_d_) } - # More respiration, less net assimilation. Sabot's data imply ratios from - # 0.0046 to 0.0302 across species against the hard-coded 0.015, so this is the + # More respiration, less net assimilation. Sabot's data imply 0.44 to 2.90 + # umol m^-2 s^-1 across their 16 species against the 1.44 default, so this is the # range a calibration actually needs, not an extreme. - expect_lt(drive(0.0302), drive(0.0046)) + expect_lt(drive(2.90)[["A"]], drive(0.44)[["A"]]) + # And the trait is the value AT 25 C: it is used verbatim there and larger above. + expect_equal(drive(0.525)[["R_d"]], 0.525) + expect_gt(drive(0.525, temp = 40)[["R_d"]], 0.525) }) diff --git a/tests/validate/compare_with_plant.R b/tests/validate/compare_with_plant.R index 067012f..c3ebed9 100644 --- a/tests/validate/compare_with_plant.R +++ b/tests/validate/compare_with_plant.R @@ -101,6 +101,17 @@ psi_soils <- c(0.5, 1.0, 2.0, 3.0, 4.0, 6.0) ppfds <- c(100, 500, 900, 1500) vpds <- c(0.5, 1.0, 2.0, 4.0) layer_counts <- c(1L, 3L, 5L) +# ⚠️ LEAF TEMPERATURE IS AN AXIS NOW (#41), not the fixed 25 C this script used to +# assume, because the golden file it reads has four temperature blocks. Two +# consequences before running anything: +# +# * at 25 C the comparison means what it always meant -- and a difference there is +# a DIFFERENT bug, since #41 is inert at the reference point by construction; +# * at 15 / 35 / 40 C phylloptim and a pre-#41 plant are EXPECTED to differ, +# because R_d's shape changed. `Leaf::rd_tracks_vcmax_` is what makes that arm +# comparable, and it lives on the phylloptim side, so an arm that uses it cannot +# be read out of the golden file -- see the arm table in this file's header. +leaf_temps <- c(15.0, 25.0, 35.0, 40.0) # Fixed drivers and traits, from plant's tests/testthat/test-leaf.r. theta <- 0.000157 @@ -111,7 +122,6 @@ rho <- 608.0 a_bio <- 0.0245 ca <- 40.0 o2 <- 21.0 -tleaf <- 25.0 patm <- 101.3 # Every constructor argument passed explicitly, matching the C++ default @@ -130,7 +140,7 @@ new_leaf <- function() { ) } -solve_one <- function(psi_soil, ppfd, vpd, layers) { +solve_one <- function(psi_soil, ppfd, vpd, layers, leaf_temp) { l <- new_leaf() i <- seq_len(layers) ps <- psi_soil + 0.25 * (i - 1) @@ -142,13 +152,14 @@ solve_one <- function(psi_soil, ppfd, vpd, layers) { PPFD = ppfd, psi_soil = ps, soil_depth = depth, leaf_specific_conductance_max = K_s * theta / h, atm_vpd = vpd, ca = ca, sapwood_volume_per_leaf_area = theta * h, - leaf_temp = tleaf, atm_o2_kpa = o2, atm_kpa = patm + leaf_temp = leaf_temp, atm_o2_kpa = o2, atm_kpa = patm ) l$find_root_collar_psi() cons <- l$soil_consumption_ data.frame( - psi_soil = psi_soil, ppfd = ppfd, vpd = vpd, layers = layers, + psi_soil = psi_soil, ppfd = ppfd, vpd = vpd, leaf_temp = leaf_temp, + layers = layers, psi_stem = l$opt_psi_stem_, opt_root_psi = l$opt_root_psi_, ci = l$ci_, assim = l$assim_colimited_, transpiration = l$transpiration_, gc = l$stom_cond_CO2_, @@ -158,15 +169,15 @@ solve_one <- function(psi_soil, ppfd, vpd, layers) { } grid <- expand.grid(layers = layer_counts, vpd = vpds, ppfd = ppfds, - psi_soil = psi_soils) + psi_soil = psi_soils, leaf_temp = leaf_temps) # expand.grid varies the FIRST column fastest; the C++ loops nest -# psi_soil > ppfd > vpd > layers, with layers innermost. Listing them in -# reverse above therefore reproduces the C++ row order. -grid <- grid[, c("psi_soil", "ppfd", "vpd", "layers")] +# leaf_temp > psi_soil > ppfd > vpd > layers, with layers innermost. Listing them +# in reverse above therefore reproduces the C++ row order. +grid <- grid[, c("psi_soil", "ppfd", "vpd", "leaf_temp", "layers")] cat(sprintf("Running plant's Leaf over %d operating points...\n", nrow(grid))) plant_rows <- do.call(rbind, Map(solve_one, grid$psi_soil, grid$ppfd, - grid$vpd, grid$layers)) + grid$vpd, grid$layers, grid$leaf_temp)) # --- compare ------------------------------------------------------------------ @@ -201,7 +212,7 @@ stopifnot(nrow(golden) == nrow(plant_rows)) # The inputs must line up before comparing outputs, or we would be comparing # different operating points and calling it agreement. -for (key in c("psi_soil", "ppfd", "vpd", "layers")) { +for (key in c("psi_soil", "ppfd", "vpd", "leaf_temp", "layers")) { if (!isTRUE(all.equal(golden[[key]], plant_rows[[key]], tolerance = 0))) { stop("grid mismatch in '", key, "': the R grid is not in the same order as ", "the C++ one, so the comparison would be meaningless") diff --git a/tools/gradient_golden.R b/tools/gradient_golden.R index 8a61502..d2671b1 100644 --- a/tools/gradient_golden.R +++ b/tools/gradient_golden.R @@ -31,10 +31,14 @@ # on Linux would just move the failure to the platform the file came from. # # These are derivatives of outputs evaluated at the ARGMAX of a flat maximum, so -# they inherit that file's sqrt-amplified class: measured worst cross-platform -# disagreement 1.3e-4, against 1.4e-4 for the same class of solved outputs. A -# central difference cancels the systematic part of a libm difference, not all of -# it. +# they inherit that file's sqrt-amplified class -- and, being finite differences, +# one amplification more. Measured worst cross-platform disagreement 1.3e-3, +# against 1.4e-4 for the solved outputs themselves. A central difference cancels +# the systematic part of a libm difference, not all of it, and what is left is +# divided by the step: the smallest-magnitude parameter in the file therefore sets +# the tolerance for all of it, which since #41 is `R_d_25` at 1.44 rather than +# `vcmax_25` at 96. `gradient_golden_tolerance()` in tests/testthat/helper-golden.R +# carries the arithmetic. suppressMessages(library(phylloptim)) # The golden grid's drivers, so every row here is an operating point the rest of @@ -59,24 +63,29 @@ grid_drivers <- function(psi_soil, ppfd = 900, vpd = 2.0, layers = 1L) { # function at all, so the composite must return EXACTLY zero for it at an # interior optimum and the fallback must return ~1.26 at a dry-pinned one. A pin # that omitted it would miss the sharpest statement of why there are two routes. +# +# `R_d_25` is in `pars` throughout because it is the smallest-magnitude parameter +# here, so it takes the smallest absolute step and sets this file's cross-platform +# tolerance -- see `gradient_golden_tolerance()`. cases <- list( list(label = "interior-1layer", args = grid_drivers(2.0), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = c("vcmax_25", "stem_b", "psi_crit", "R_d_25")), list(label = "interior-5layer", args = grid_drivers(0.5, vpd = 0.5, layers = 5L), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = c("vcmax_25", "stem_b", "psi_crit", "R_d_25")), list(label = "pinned-dry-3layer", args = grid_drivers(4.0, vpd = 0.5, layers = 3L), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = c("vcmax_25", "stem_b", "psi_crit", "R_d_25")), list(label = "shutdown-1layer", args = grid_drivers(6.0), - pars = c("vcmax_25", "stem_b", "psi_crit")), + pars = c("vcmax_25", "stem_b", "psi_crit", "R_d_25")), list(label = "single-potential", args = list(psi_soil = 1.5, PPFD = 900, atm_vpd = 2.0, supply = leaf_supply_single(), root_network = series_resistance(1e4)), - pars = c("vcmax_25", "leaf_specific_conductance_max", "resistance")) + pars = c("vcmax_25", "leaf_specific_conductance_max", "resistance", + "R_d_25")) ) out <- do.call(rbind, lapply(cases, function(cs) { diff --git a/vignettes/cpp-interface.Rmd b/vignettes/cpp-interface.Rmd index b2d55b4..9f95151 100644 --- a/vignettes/cpp-interface.Rmd +++ b/vignettes/cpp-interface.Rmd @@ -120,7 +120,7 @@ d.root_network = roots; d.PPFD = 900; d.psi_soil = {2.0}; d.soil_depth = {1.0}; d.atm_vpd = 2.0; d.ca = 40.0; d.leaf_temp = 25.0; d.atm_o2_kpa = 21.0; d.atm_kpa = 101.3; -double theta[g::n_pars] = {/* 13 traits, then kmax, then resistance */}; +double theta[g::n_pars] = {/* 14 traits, then kmax, then resistance */}; const int pars[1] = {0}; // g::par_names()[0] == "vcmax_25" phylloptim::Leaf l; @@ -130,10 +130,12 @@ const std::vector out = // out[i].status is Interior / Pinned / NoGradient / Error ``` -`theta` is `g::n_pars` = 15 doubles: the thirteen traits in `set_traits`' argument +`theta` is `g::n_pars` = 16 doubles: the fourteen traits in `set_traits`' argument order, then `leaf_specific_conductance_max`, then the single-potential path's -`resistance`. `g::par_names()` is that order, and `pars` holds positions into it — -⚠️ appending to the enumeration is safe and reordering it is not. +`resistance`. `g::par_names()` is that order and every position has a name +(`g::par_vcmax_25`, `g::par_R_d_25`, `g::par_kmax`, ...); `pars` holds positions into +it. ⚠️ R indexes these positions, so reordering the enumeration silently +differentiates the wrong parameter. Three things the free function gives you that a hand-rolled loop would not: @@ -157,7 +159,7 @@ The ingredients are still public, if you want to compose something else: | piece | what it is | |---|---| -| `set_traits(...)` | replace all thirteen traits, refreshing splines and the temperature cache | +| `set_traits(...)` | replace all fourteen traits, refreshing splines and the temperature cache | | `perturb_stem_b(b)` | move `stem_b` by rescaling the curve instead of rebuilding it | | `dprofit_droot_collar_psi(psi, &feasible)` | dprofit/dψ at a given collar potential | | `evaluate_root_collar_psi(psi)` | solve the inner problem at a fixed collar | diff --git a/vignettes/phylloptim.Rmd b/vignettes/phylloptim.Rmd index 4c4ba27..c2631b6 100644 --- a/vignettes/phylloptim.Rmd +++ b/vignettes/phylloptim.Rmd @@ -338,9 +338,13 @@ dim(leaf_gradient(psi_soil = 2.0, PPFD = 900)$gradient) rownames(leaf_gradient(psi_soil = 2.0, PPFD = 900)$gradient) ``` -Fourteen on the multi-layer path — the thirteen traits from `leaf_traits()`, plus +Fifteen on the multi-layer path — the fourteen traits from `leaf_traits()`, plus `leaf_specific_conductance_max`, which is not a trait but is fitted like one. The -single-potential path adds `resistance`, making fifteen. +single-potential path adds `resistance`, making sixteen. + +`R_d_25`, dark respiration at 25 °C, is one of those fourteen and behaves like any +other trait. So `dY/dvcmax_25` is a **partial** derivative at fixed respiration: a +fit that wants respiration to follow Vcmax moves both and adds the two columns. **Selecting fewer genuinely costs less**: the work is one solve plus two cheap evaluations per parameter, so it scales with what you ask for. @@ -353,7 +357,12 @@ bench <- function(pars) { as.numeric(Sys.time() - t0, units = "secs") / 20 * 1000 } tibble::tibble( - request = c("`pars = NULL` (all 16)", "4 parameters", "1 parameter"), + # Counted, not written down: this label said 16 for a while when the answer was + # 14, which is exactly the way a number beside a chunk rots (the chunk runs, the + # prose next to it is never asserted). + request = c(sprintf("`pars = NULL` (all %d)", + nrow(leaf_gradient(psi_soil = 2.0, PPFD = 900)$gradient)), + "4 parameters", "1 parameter"), `ms per call` = round(c(bench(NULL), bench(c("vcmax_25", "jmax_25", "stem_b", "cost_scale_TF24")),