From 87d3a4bb411b49795cfc6177db7438e104c2247b Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 20 Aug 2026 08:57:05 +1000 Subject: [PATCH 1/3] One molar mass of water, not two kg_to_mol_h2o was 55.4939 and kg_per_mol_h2o was 0.018015: two constants naming the same quantity in opposite directions, disagreeing by 0.0277%, used in opposite halves of the model. A flux converted kg -> mol on the demand side and mol -> kg on the supply side did not come back. Which was wrong is not a convention question. 55.4939 is 1/0.018020, a molar mass of 18.0200 g/mol; water's is 18.015 (2(1.008) + 15.999). So there is now one molar_mass_h2o = 0.018015 and both old names derive from it, reciprocal by construction. Both names are kept: plant using-declares both (#51). Moves results: 3710 of 5184 golden cells, median 9.4e-05, of which 3377 within 2x the constant's own 2.77e-04; largest absolute move 1.6e-03. Gradients 60 of 100, worst 2.9e-03. Full split in the first PR comment. Version to 0.4.0, per the rule #99 set. Co-Authored-By: Claude Opus 5 (1M context) --- DESCRIPTION | 2 +- NEWS.md | 38 + R/fingerprint.R | 2 +- inst/include/phylloptim/constants.hpp | 40 +- tests/cpp/golden/operating_points.tsv | 960 +++++++++++++------------- tests/cpp/test_leaf.cpp | 63 +- tests/testthat/gradient_golden.tsv | 28 +- tests/testthat/test-golden.R | 44 +- tests/testthat/test-gradient.R | 46 +- 9 files changed, 680 insertions(+), 543 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1b36306..7cf98cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: phylloptim Title: Leaf Gas Exchange with Explicit Plant Hydraulics -Version: 0.3.0 +Version: 0.4.0 Authors@R: c( person("Isaac", "Towers", , "", "aut", comment = "Author of the leaf gas exchange and hydraulics model"), diff --git a/NEWS.md b/NEWS.md index 7254c35..a197eae 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,41 @@ +# phylloptim 0.4.0 + +## One molar mass of water, so the kg <-> mol conversions are reciprocal (#51) — MOVES RESULTS + +`kg_to_mol_h2o` was 55.4939 and `kg_per_mol_h2o` was 0.018015 — two constants naming +the same physical quantity in opposite directions, disagreeing by **0.0277%**, used in +opposite halves of the model. The demand side converted transpiration kg -> mol with +the first; the supply side converted uptake mol -> kg with the second. So a water flux +pushed through both did not come back. The header said the discrepancy was deliberate, +"kept at the historical 0.018015 to preserve results". + +**Which one was wrong is not a matter of convention, which is what let this be settled +rather than argued.** 55.4939 is 1/0.018020, i.e. it encodes a molar mass of 18.0200 +g/mol. The molar mass of water is 18.015 g/mol — from the standard atomic weights, +2(1.008) + 15.999. So `0.018015` is the physical value and the forward constant was the +odd one. There is now one `molar_mass_h2o = 0.018015` and both old names are derived +from it, reciprocal by construction; both names are kept because plant `using`-declares +both. + +Note this is the **larger** of the two possible moves — unifying the other way would +have preserved more digits by adopting a molar mass water does not have. + +**Blast radius.** 3710 of 5184 golden cells, median relative move 9.4e-05, and **3377 +of the 3710 move by no more than 2x the constant's own 2.77e-04** — i.e. the bulk is +that constant propagating. The largest **absolute** move anywhere in the file is +1.6e-03. The 184 cells whose relative move exceeds 1e-03 are near-zero quantities: the +worst, 2.7e-02, is `profit` = 0.0088 at a 40 C five-layer point where benefit nearly +cancels cost. Recorded gradients: 60 of 100 cells, median 3.2e-04, worst 2.9e-03. +⚠️ That worst is the same order as the gradient file's own cross-platform disagreement +(~2.3e-03), so **off macOS/arm64 this change is not cleanly separable from noise in +that file.** + +Directionally: the forward constant rose 0.0277%, so conductance per unit transpiration +rose with it, and the leaf buys slightly more carbon for the same water. + +⚠️ **plant's `LinkingTo: phylloptim (>= 0.2.0)` floor is now three minor versions +stale**, and this is a results change it should be able to require. `>= 0.4.0`. + # phylloptim 0.3.0 ⚠️ **This section was headed `0.2.1` until now, and the renumbering is the point of diff --git a/R/fingerprint.R b/R/fingerprint.R index 3af5b8b..6881112 100644 --- a/R/fingerprint.R +++ b/R/fingerprint.R @@ -56,7 +56,7 @@ leaf_behaviour_fingerprint <- function() { # ⚠️ GENERATED. Regenerate with tools/fingerprint.R after regenerating a golden # file, and never by hand -- test-fingerprint.R recomputes it and fails on a # mismatch, which is the whole mechanism. - "7a0f1e194fc8" + "e4f5a6ebd157" } # The digest itself, in one place so the exported constant above, the regeneration diff --git a/inst/include/phylloptim/constants.hpp b/inst/include/phylloptim/constants.hpp index d99448c..99033ef 100644 --- a/inst/include/phylloptim/constants.hpp +++ b/inst/include/phylloptim/constants.hpp @@ -56,12 +56,40 @@ inline constexpr double ko_ha = 36.38e3; // Leaf::umol_per_mol_to_Pa_, derived from atm_kpa_. The old `0.1013` was 101.3 // kPa hard-coded; don't reinstate it. -// mol H2o kg ^-1 -inline constexpr double kg_to_mol_h2o = 55.4939; -// kg mol^-1: molar mass of water, for converting molar water flux back to kg. -// (Intentionally distinct from 1/kg_to_mol_h2o, which it does not exactly equal; -// kept at the historical 0.018015 to preserve results.) -inline constexpr double kg_per_mol_h2o = 0.018015; +// The molar mass of water, and the ONE place it is written down (#51). Everything +// that crosses between a kg basis and a mol basis is derived from this, so the two +// directions are reciprocal by construction and a round trip is the identity to +// within one rounding. +// +// ⚠️ THIS USED TO BE TWO INDEPENDENT NUMBERS THAT DISAGREED BY 0.0277%, and the +// header said so on purpose: `kg_to_mol_h2o` was 55.4939 while `kg_per_mol_h2o` was +// 0.018015, with a comment recording that the first was "intentionally distinct +// from 1/kg_to_mol_h2o ... kept at the historical 0.018015 to preserve results". +// Two constants naming the same physical quantity in opposite directions, used in +// opposite halves of the model: the demand side converted transpiration kg -> mol +// with the first, the supply side converted uptake mol -> kg with the second. +// +// WHICH ONE WAS WRONG IS NOT A MATTER OF CONVENTION, which is what let this be +// settled rather than argued. 55.4939 is 1/0.018020, i.e. it encodes a molar mass of +// 18.0200 g/mol. The molar mass of water is 18.015 g/mol -- from the standard atomic +// weights, 2(1.008) + 15.999 -- so 0.018015 is the physical value and the forward +// constant was the odd one. Unifying therefore moves `kg_to_mol_h2o` from 55.4939 to +// 55.509298..., which is the LARGER of the two possible moves, and it is still the +// right one: the alternative preserves more digits by adopting a molar mass water +// does not have. +// +// It also happens to leave plant's `using ::phylloptim::kg_per_mol_h2o` -- +// tf24_strategy.cpp's water consumption rate, the only live use of either name over +// there -- multiplying by an unchanged constant. That is a convenience, not the +// reason; plant's results still move, because the leaf's operating point does. +// +// Both old names are kept, and deliberately: plant `using`-declares both, so +// deleting either would break its build for no benefit. +inline constexpr double molar_mass_h2o = 0.018015; // kg mol^-1 +// kg mol^-1, for converting a molar water flux back to kg. +inline constexpr double kg_per_mol_h2o = molar_mass_h2o; +// mol H2O kg^-1 -- the reciprocal, now genuinely so. +inline constexpr double kg_to_mol_h2o = 1.0 / molar_mass_h2o; // mol mol ^-1 / (umol mol ^-1) inline constexpr double umol_to_mol = 1e-6; // Pa kPa^-1 diff --git a/tests/cpp/golden/operating_points.tsv b/tests/cpp/golden/operating_points.tsv index 42556f5..ab0b052 100644 --- a/tests/cpp/golden/operating_points.tsv +++ b/tests/cpp/golden/operating_points.tsv @@ -1,244 +1,244 @@ psi_soil ppfd vpd leaf_temp layers psi_stem opt_root_psi ci assim transpiration gc profit e_up uptake -0.5 100 0.5 25 1 1.4064315157230904 1.1397291800324896 33.535719423557367 3.4216414573490117 7.9644452142332613e-06 0.053619621786311737 3.3030570555526007 7.9644455320981566e-06 0.00044210077891191545 -0.5 100 0.5 25 3 1.5954124971659924 1.4018117298270361 31.191249087006774 3.2939585898339492 5.6265869403364712e-06 0.037880286143406765 3.1008759409911346 5.6265870700498279e-06 0.00031232789731056498 -0.5 100 0.5 25 5 1.7452545545113272 1.5881353349338976 29.26221372465977 3.1770775521522618 4.4519911133823949e-06 0.029972468046986989 2.905100614955062 4.451991550411658e-06 0.00024712692480775232 -0.5 100 1 25 1 1.5932824843611659 1.2671223542432744 29.87940784684681 3.2157448245139046 9.5619590523274327e-06 0.032187340996817651 3.0236501713776431 9.5619591422393109e-06 0.00053077763764858787 -0.5 100 1 25 3 1.792089936227345 1.5523575254639304 26.688926403109683 3.0013314142961085 6.7853474838497329e-06 0.022840747596739566 2.7006930858511771 6.7853474843817958e-06 0.00037664987423712438 -0.5 100 1 25 5 1.9404992363787303 1.7453156059561366 24.229209988285525 2.8076762493713692 5.3575323613880689e-06 0.01803445508120111 2.402599334908301 5.3575325764326462e-06 0.00029739287129795425 -0.5 100 2 25 1 1.796754883224458 1.403064367266345 24.76324542098623 2.8521396964186105 1.126625405696789e-05 0.018962158230542696 2.5485370769014071 1.1266254107284797e-05 0.0006253818544149207 -0.5 100 2 25 3 1.9747505017184552 1.6895987603563816 20.87490954522567 2.4917019650291881 7.841403756284557e-06 0.013197815176578472 2.0594485162722274 7.8414043294004458e-06 0.00043527084814878967 -0.5 100 2 25 5 2.0812347115368217 1.8568575136921996 18.155583441976784 2.1776498358393592 5.9999663789796969e-06 0.010098504017471897 1.6531924903518349 5.9999667351424585e-06 0.00033305394033541266 -0.5 100 4 25 1 1.9478356888215438 1.5017496970624515 18.55403408854426 2.2275821156610927 1.2503146687341737e-05 0.010521982047725425 1.8167837670905356 1.2503147133216547e-05 0.00069404091774724098 -0.5 100 4 25 3 2.0130156381644104 1.7179877325704673 14.788296988437237 1.6880916255969911 8.059814529785612e-06 0.0067827104577008659 1.2240623501463697 8.0598148848335208e-06 0.00044739466471460014 -0.5 100 4 25 5 2.0063215670071219 1.7976840658200517 12.604399811198828 1.2879603966247419 5.6591721458135337e-06 0.0047624577406199832 0.82959875184286114 5.6591722813330827e-06 0.00031413667950780366 -0.5 500 0.5 25 1 2.4109901172055292 1.7891385804115763 26.953803399175321 13.962350236233943 1.610333535058437e-05 0.10841367198476014 13.074476999673436 1.6103335351217076e-05 0.00089388483770286298 -0.5 500 0.5 25 3 2.7164829891260012 2.2105108140029675 23.551280527047631 12.950185456809193 1.1846365343788535e-05 0.079754158913824924 11.617786198957639 1.1846366710650659e-05 0.00065758349767697244 -0.5 500 0.5 25 5 2.9416567539753897 2.491798670544096 21.156049380602155 12.089414780959574 9.6532721227129898e-06 0.064989435710500656 10.366287275475116 9.6532733143316015e-06 0.00053584642322129349 -0.5 500 1 25 1 2.7771547107039507 1.9960803050999467 20.778763228621415 11.939993582679428 1.8693644905798955e-05 0.062926302001880804 10.507323310430502 1.8693645986015434e-05 0.0010376711621435156 -0.5 500 1 25 3 3.0330102014283211 2.408646900778213 17.044362096260372 10.197210725095688 1.3367901976221861e-05 0.044998856088591353 8.3018317586369346 1.3367901981834845e-05 0.00074204285216957226 -0.5 500 1 25 5 3.1583294361732412 2.6343326757137708 14.723041592297534 8.7962094107029394 1.0472297472000246e-05 0.035251710230795992 6.6531341193001463 1.0472298027020679e-05 0.00058130990990955755 -0.5 500 2 25 1 2.9462904096973555 2.08444288084937 14.248433530867034 8.4712366920423126 1.9799051423878862e-05 0.033323653453567123 6.7395524994711717 1.9799052300281291e-05 0.0010990314904402603 -0.5 500 2 25 3 2.9225815548173113 2.3414998122240656 11.309881631845681 6.1265377221241764 1.2852392837171983e-05 0.021631777997125925 4.4384260644956592 1.2852394389878127e-05 0.00071342738772568011 -0.5 500 2 25 5 2.833110915061622 2.4173177253909621 9.7364229966751381 4.6386409369410035 9.2251134932392196e-06 0.015526727949591018 3.1101510785484425 9.225113757567589e-06 0.00051207958687580287 -0.5 500 4 25 1 2.6402150326898215 1.9210741314244792 9.5836913521964231 4.4863829806344899 1.7755015392816984e-05 0.014941674915279089 3.2745250391091312 1.7755016415853437e-05 0.00098556849380257764 -0.5 500 4 25 3 2.4363561900592154 2.0218974856044238 7.9399765537702125 2.7690999438141248 1.0396951317153062e-05 0.0087495202484438143 1.8482539356547472 1.0396952294769454e-05 0.00057712752121950894 -0.5 500 4 25 5 2.2867611239124748 2.016583635196457 7.1431380235951467 1.8887638024633771 6.919628565917434e-06 0.0058231907029630183 1.1519511946939383 6.9196289469185034e-06 0.00038410374393108541 -0.5 900 0.5 25 1 2.7197604410447243 1.9650087070302278 26.048188942300374 16.972876943369208 1.8304847057311835e-05 0.12323507157978875 15.635159184548733 1.830484847919428e-05 0.0010160892855506122 -0.5 900 0.5 25 3 3.0590453936785567 2.4241509568611108 22.789749720102598 15.426180066088714 1.3486909354637241e-05 0.090798914326079339 13.480384375876319 1.3486910990082833e-05 0.00074864895865017116 -0.5 900 0.5 25 5 3.2874061407846247 2.7150123329803346 20.561732192903506 14.127399787118728 1.0935682742199735e-05 0.073623103284576483 11.717131613072453 1.0935684088448875e-05 0.00060703214479316538 -0.5 900 1 25 1 3.0845830084812849 2.1529681238294742 19.972253675990459 13.746976173505795 2.06560046157449e-05 0.069531971488310168 11.751181815875075 2.0656005529640378e-05 0.0011466003624557523 -0.5 900 1 25 3 3.2552167071314595 2.5367564606412847 16.514782254357939 11.199702974192977 1.4351032161804206e-05 0.048308256009092082 8.8571004956490977 1.4351033237008381e-05 0.00079661577779674615 -0.5 900 1 25 5 3.3008316449749167 2.7232113254639776 14.362616300819996 9.3565169518213729 1.098276597094949e-05 0.036970042588621105 6.9178393586801432 1.0982766210598657e-05 0.00060964564033298121 -0.5 900 2 25 1 3.0506148929043242 2.1364568870268812 13.845359547567949 8.8865087986354592 2.0449544585256969e-05 0.034418494222430207 6.957100827264993 2.0449545713341124e-05 0.0011351399230275395 -0.5 900 2 25 3 2.9571261757000635 2.3627422523318611 11.11699827965273 6.2459967187747658 1.3015493666290375e-05 0.021906291931716535 4.4942259637785442 1.3015493821534184e-05 0.00072248092264969109 -0.5 900 2 25 5 2.8486017197938178 2.4280650238146269 9.6208634276353742 4.68754060377894 9.2869014270161226e-06 0.01563072281523949 3.1319705838605314 9.2869027021207833e-06 0.00051550944780021004 -0.5 900 4 25 1 2.6522498945103776 1.9277849481905887 9.4686138378274354 4.5246599673936974 1.7839005529437747e-05 0.015012356539018206 3.2941949963470192 1.7839006888533563e-05 0.00099023074596356168 -0.5 900 4 25 3 2.4404897779944061 2.0247605801731612 7.8817725565409198 2.7799994163068651 1.0418959521538034e-05 0.0087680411805925017 1.8537118747795378 1.0418960614863737e-05 0.00057834918761386273 -0.5 900 4 25 5 2.2889167997028221 2.0182367568797099 7.104156810751153 1.8936052214909869 6.9291447675929812e-06 0.0058311990312420112 1.1543186116999453 6.9291452468914118e-06 0.00038463198706030596 -0.5 1500 0.5 25 1 2.8799224461320598 2.0503524385318022 25.954225797283264 18.083941475864073 1.9372632441163029e-05 0.13042380185427585 16.472899690884802 1.9372633102666619e-05 0.0010753612602090823 -0.5 1500 0.5 25 3 3.1949269863757817 2.50295922490713 22.736487599463125 16.167837514687886 1.4091719930031557e-05 0.094870725159437785 13.950159453241458 1.4091721595786804e-05 0.00078222157067925639 -0.5 1500 0.5 25 5 3.3913677928808488 2.7775205859597065 20.515385285153553 14.625846867062355 1.1294588890250263e-05 0.076039393609589903 11.992938265924806 1.1294589877454459e-05 0.00062695475311987006 -0.5 1500 1 25 1 3.1648920581658251 2.1911568882113466 19.864151222823153 14.140651868278066 2.1133465216675257e-05 0.071139193093275113 11.984270231861233 2.1133465338826787e-05 0.0011731038211949369 -0.5 1500 1 25 3 3.2906228580384393 2.5562593578505401 16.437390000784326 11.353759436412837 1.4500651567003244e-05 0.048811902886110474 8.936694285509013 1.4500652644111865e-05 0.00080492104602341739 -0.5 1500 1 25 5 3.3195393624420411 2.7345742020498625 14.306787609941376 9.4325989070892042 1.1048013206765571e-05 0.037189676977015688 6.9541571676104059 1.1048013895288418e-05 0.00061326749349366739 -0.5 1500 2 25 1 3.0635838198654595 2.142785760963382 13.785500843577079 8.9413159149529715 2.0528683290124271e-05 0.034551692056978056 6.9866737482811869 2.0528685055245255e-05 0.0011395328923255762 -0.5 1500 2 25 3 2.9618081449919673 2.3656048925914694 11.084785084920597 6.263521857755423 1.3037472107710841e-05 0.021943283702163766 4.5030388889266248 1.3037472113595274e-05 0.0007237009222090077 -0.5 1500 2 25 5 2.8510249480242753 2.4297427398960521 9.5996738299495856 4.6956820147320624 9.2965467100300342e-06 0.015646956727750547 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0.0084985919051466449 -4.0370681668915509 1.2619992408588916e-06 7.0052691693527148e-05 +4 500 0.5 40 5 4.6301677825497327 4.4905618036218797 26.652177739572423 0.84881221343040503 9.5658143266459546e-07 0.0064418506287291216 -4.4699299575895388 9.5658247986218864e-07 5.3099221751994928e-05 +4 500 1 40 1 4.1951244374765571 4.0893904042288778 25.016521184166294 0.5098258791835808 1.0236699537575632e-06 0.0034468204744762315 -3.9203411253003915 1.02367039530339e-06 5.6823224829497089e-05 +4 500 1 40 3 4.2360334788521001 4.2075807424608413 23.291430387170248 0.14383926895721366 2.5899354036975174e-07 0.000872062557298587 -4.3748260377047909 2.5899613930951775e-07 1.4376693827894409e-05 +4 500 1 40 5 4.3192648651884964 4.3192647263053008 22.623841558636435 6.7529481695416393e-07 1.1692042524380496e-12 3.9368520501702478e-09 -4.6960326754589357 3.1036885690132533e-12 1.7228357307872626e-10 +4 500 2 40 1 4.0051745686255105 4.0050287756412137 22.625923343373696 0.00045107326176196949 1.5621620535007706e-09 2.6299942333422758e-06 -4.0097830965281336 1.5626505833126274e-09 8.6741636597980988e-08 +4 500 2 40 3 4.1729334888883658 4.1729333291926638 22.623840452901941 4.3606405775165058e-07 1.510000983184767e-12 2.5421779188769322e-09 -4.3818313398012902 4.0159515427695062e-12 2.2292265016761069e-10 +4 500 2 40 5 4.3192648651884964 4.3192647263053008 22.623839998016244 3.37647437120836e-07 1.1692042524380496e-12 1.9684260250851239e-09 -4.696033013106315 3.1036885690132533e-12 1.7228357307872626e-10 +4 500 4 40 1 4.0051745686255105 4.0050287756412137 22.624880946249633 0.00022555016246306181 1.5621620535007706e-09 1.3149971166711379e-06 -4.0100086196274329 1.5626505833126274e-09 8.6741636597980988e-08 +4 500 4 40 3 4.1729334888883658 4.1729333291926638 22.623839445148931 2.180320426425908e-07 1.510000983184767e-12 1.2710889594384661e-09 -4.3818315578333049 4.0159515427695062e-12 2.2292265016761069e-10 +4 500 4 40 5 4.3192648651884964 4.3192647263053008 22.623839217706067 1.6882372788629141e-07 1.1692042524380496e-12 9.8421301254256194e-10 -4.6960331819300247 3.1036885690132533e-12 1.7228357307872626e-10 +4 900 0.5 40 1 4.3637602535176336 4.1563537240339157 28.933350664814022 1.3482522043860352 1.8326339686483953e-06 0.012341400198708823 -3.4409706470963415 1.8326360416094828e-06 0.00010172833980624384 +4 900 0.5 40 3 4.5145402328090105 4.3462058096435996 27.566809837864163 1.06809745726274 1.2922574571602242e-06 0.0087023741300300793 -4.0272506517198092 1.2922600695410419e-06 7.173244904474282e-05 +4 900 0.5 40 5 4.6383816577844357 4.4946593948753906 26.620147543312243 0.87114146017591176 9.793954930110406e-07 0.0065954860265825324 -4.4630623424257845 9.7939745654775056e-07 5.4365665087302274e-05 +4 900 1 40 1 4.1998502315828361 4.0913686526435002 24.97382425706234 0.52323038562806445 1.0475993747469715e-06 0.0035273937275114454 -3.9172009522394804 1.0475994653490604e-06 5.8151510704915924e-05 +4 900 1 40 3 4.2393486506215128 4.2093685503679952 23.248863427451575 0.15164235925887493 2.7234975612924419e-07 0.00091703455024646585 -4.3741584631394224 2.7235234690649764e-07 1.5118087532972393e-05 +4 900 1 40 5 4.3192648651884964 4.3192647263053008 22.554094925683799 6.7800540204387971e-07 1.1692042524380496e-12 3.9368520501702478e-09 -4.6960326727483501 3.1036885690132533e-12 1.7228357307872626e-10 +4 900 2 40 1 4.0051745686255105 4.0050287756412137 22.556159205459522 0.0004528845083595634 1.5621620535007706e-09 2.6299942333422758e-06 -4.0097812852815355 1.5626505833126274e-09 8.6741636597980988e-08 +4 900 2 40 3 4.1729334888883658 4.1729333291926638 22.554093829246511 4.3781438785472915e-07 1.510000983184767e-12 2.5421779188769322e-09 -4.3818313380509597 4.0159515427695062e-12 2.2292265016761069e-10 +4 900 2 40 5 4.3192648651884964 4.3192647263053008 22.55409337818557 3.3900273210818455e-07 1.1692042524380496e-12 1.9684260250851239e-09 -4.6960330117510196 3.1036885690132533e-12 1.7228357307872626e-10 +4 900 4 40 1 4.0051745686255105 4.0050287756412137 22.555125573713347 0.00022645567197399075 1.5621620535007706e-09 1.3149971166711379e-06 -4.010007714117922 1.5626505833126274e-09 8.6741636597980988e-08 +4 900 4 40 3 4.1729334888883658 4.1729333291926638 22.554092829966844 2.1890720658390705e-07 1.510000983184767e-12 1.2710889594384661e-09 -4.3818315569581419 4.0159515427695062e-12 2.2292265016761069e-10 +4 900 4 40 5 4.3192648651884964 4.3192647263053008 22.554092604436363 1.695013764901887e-07 1.1692042524380496e-12 9.8421301254256194e-10 -4.6960331812523757 3.1036885690132533e-12 1.7228357307872626e-10 +4 1500 0.5 40 1 4.3669626232335776 4.1575532969779854 28.924719298202675 1.3599588625501604 1.8471057971074764e-06 0.01243885699023185 -3.4359239953823155 1.8471081290030254e-06 0.00010253167521526647 +4 1500 0.5 40 3 4.5174222694942712 4.3475165314795214 27.556403076567619 1.0770537536459641 1.3020036019532416e-06 0.0087680070252742388 -4.0239884309631506 1.3020061384790789e-06 7.2273446487875593e-05 +4 1500 0.5 40 5 4.6410721487912978 4.4959967050906151 26.608943692200363 0.87849862078330743 9.868405569993324e-07 0.0066456228873830944 -4.4607575653303133 9.8684275749511258e-07 5.4778948514854987e-05 +4 1500 1 40 1 4.2014274340123121 4.0920275755626223 24.959175727740934 0.52772504027359757 1.0555694246202684e-06 0.0035542298488462939 -3.9161296230365346 1.0555694513665657e-06 5.859391903228231e-05 +4 1500 1 40 3 4.2404866513667763 4.2099814983739314 23.23424610311865 0.15432646832837671 2.7692876470328293e-07 0.00093245262562111617 -4.373922477173398 2.7693133054602887e-07 1.5372263699474266e-05 +4 1500 1 40 5 4.3192648651884964 4.3192647263053008 22.53013435120867 6.7893659005946461e-07 1.1692042524380496e-12 3.9368520501702478e-09 -4.6960326718171626 3.1036885690132533e-12 1.7228357307872626e-10 +4 1500 2 40 1 4.0051745686255105 4.0050287756412137 22.53219312373627 0.00045350672609911769 1.5621620535007706e-09 2.6299942333422758e-06 -4.0097806630637969 1.5626505833126274e-09 8.6741636597980988e-08 +4 1500 2 40 3 4.1729334888883658 4.1729333291926638 22.530133257696423 4.3841568819757981e-07 1.510000983184767e-12 2.5421779188769322e-09 -4.3818313374496594 4.0159515427695062e-12 2.2292265016761069e-10 +4 1500 2 40 5 4.3192648651884964 4.3192647263053008 22.530132807838818 3.3946832544984318e-07 1.1692042524380496e-12 1.9684260250851239e-09 -4.6960330112854267 3.1036885690132533e-12 1.7228357307872626e-10 +4 1500 4 40 1 4.0051745686255105 4.0050287756412137 22.531162249644908 0.00022676674504662486 1.5621620535007706e-09 1.3149971166711379e-06 -4.0100074030448489 1.5626505833126274e-09 8.6741636597980988e-08 +4 1500 4 40 3 4.1729334888883658 4.1729333291926638 22.530132261082635 2.1920786075213528e-07 1.510000983184767e-12 1.2710889594384661e-09 -4.3818315566574872 4.0159515427695062e-12 2.2292265016761069e-10 +4 1500 4 40 5 4.3192648651884964 4.3192647263053008 22.530132036153802 1.6973417027443816e-07 1.1692042524380496e-12 9.8421301254256194e-10 -4.6960331810195814 3.1036885690132533e-12 1.7228357307872626e-10 6 100 0.5 40 1 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 6 100 0.5 40 3 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 6 100 0.5 40 5 5.8702829999999997 5.8702829999999997 8.9954794232730979 -3.1707025955141233 0 0 -10.115293908969731 0 0 diff --git a/tests/cpp/test_leaf.cpp b/tests/cpp/test_leaf.cpp index 4d4ff3c..b471a90 100644 --- a/tests/cpp/test_leaf.cpp +++ b/tests/cpp/test_leaf.cpp @@ -274,15 +274,24 @@ void test_solve_single_layer() { ok(l.opt_psi_stem_ <= l.psi_crit, "stem stays within psi_crit"); ok(l.transpiration_ > 0.0, "transpiration is positive"); ok(l.assim_colimited_ > 0.0, "assimilation is positive"); - // Regression guards -- see the note at the top of this file. Moved by PLAN 11a - // (the collar root-find): opt_psi_stem_ 3.595247 -> 3.595088 and - // assim_colimited_ 5.599511 -> 5.599153, both ~1e-4 relative, which is the - // argmax correction and not rounding. profit_ and transpiration_ did not move at - // this tolerance -- profit_ because it is the maximum and therefore flat. - near(l.opt_psi_stem_, 3.595088, 1e-5, "opt_psi_stem_"); - near(l.assim_colimited_, 5.599153, 1e-5, "assim_colimited_"); + // Regression guards -- see the note at the top of this file. Moved twice: + // + // PLAN 11a, the collar root-find: opt_psi_stem_ 3.595247 -> 3.595088 and + // assim_colimited_ 5.599511 -> 5.599153, both ~1e-4 relative, which is the + // argmax correction and not rounding. profit_ and transpiration_ did not move + // at this tolerance -- profit_ because it is the maximum and therefore flat. + // + // #51, unifying the kg <-> mol water constants on the molar mass of water: + // opt_psi_stem_ -> 3.595332, assim_colimited_ -> 5.601016, profit_ 2.515843 -> + // 2.517157. The forward constant rose 0.0277%, so conductance-per-unit- + // transpiration rose with it, and the leaf buys more carbon for the same water. + // ⚠️ profit_ DID move this time, by 5.2e-04, which is the largest of the three: + // the flat-maximum argument protects the maximum against a displacement of its + // LOCATION, not against the objective itself being rescaled. + near(l.opt_psi_stem_, 3.595332, 1e-5, "opt_psi_stem_"); + near(l.assim_colimited_, 5.601016, 1e-5, "assim_colimited_"); near(l.transpiration_, 1.141941e-05, 1e-5, "transpiration_"); - near(l.profit_, 2.515843, 1e-5, "profit_"); + near(l.profit_, 2.517157, 1e-5, "profit_"); } void test_solve_is_deterministic() { @@ -2477,6 +2486,43 @@ bool mentions(const std::string& haystack, const char* needle) { // before, which is exactly why the accumulating `psi += step` loop could drop its // last knot for years: the shortfall is invisible from outside unless the domain // edge is compared with the function that is supposed to define it. +// The kg <-> mol water conversions are reciprocal, and the round trip is the +// identity (#51). They used to be two independently written numbers disagreeing by +// 0.0277%, used in opposite halves of the model -- the demand side converting +// transpiration kg -> mol, the supply side converting uptake mol -> kg -- so a flux +// pushed through both did not come back. +// +// Asserted rather than left to the header comment, because "these two constants are +// reciprocals" is exactly the kind of claim that was already written down here and +// was false. +void test_water_mass_conversions_are_reciprocal() { + printf("kg <-> mol water conversions\n"); + // Exact to the last bit in one direction: kg_to_mol_h2o IS 1/molar_mass_h2o. + ok(phylloptim::kg_to_mol_h2o == 1.0 / phylloptim::molar_mass_h2o, + "kg_to_mol_h2o is exactly the reciprocal of the molar mass"); + ok(phylloptim::kg_per_mol_h2o == phylloptim::molar_mass_h2o, + "kg_per_mol_h2o IS the molar mass, not a second copy of it"); + + // The round trip cannot be bit-exact -- 1/x then *x is not the identity for most + // x -- so the claim is that it is within one rounding, which is what "reciprocal" + // can actually buy. Before #51 this was out by 2.8e-04. + for (double kg : {1e-9, 1e-6, 1e-3, 1.0, 1e3}) { + const double round_trip = kg * phylloptim::kg_to_mol_h2o * + phylloptim::kg_per_mol_h2o; + near(round_trip, kg, 4.0 * std::numeric_limits::epsilon(), + "kg -> mol -> kg returns the input at " + + phylloptim::util::format_double(kg)); + } + + // And the value is the molar mass of water, not a neighbouring one: 18.015 g/mol + // from the standard atomic weights, 2(1.008) + 15.999. The pre-#51 forward + // constant implied 18.0200, which is what this pins against. + near(phylloptim::molar_mass_h2o * 1000.0, 18.015, 1e-9, + "the molar mass is water's, in g/mol"); + ok(std::abs(phylloptim::kg_to_mol_h2o - 55.4939) > 1e-3, + "the forward constant is no longer the pre-#51 55.4939"); +} + void test_knot_grid_reaches_its_intended_domain() { printf("vulnerability knot grid\n"); const double resolutions[] = {10.0, 50.0, 100.0, 200.0, 1000.0}; @@ -2753,6 +2799,7 @@ int main() { test_rd_temperature_response(); test_set_traits_matches_a_fresh_leaf(); test_perturb_stem_b_matches_a_rebuild(); + test_water_mass_conversions_are_reciprocal(); test_knot_grid_reaches_its_intended_domain(); test_psi_crit_must_lie_on_the_stem_curve(); test_bad_input_throws(); diff --git a/tests/testthat/gradient_golden.tsv b/tests/testthat/gradient_golden.tsv index 85adb38..2d0e147 100644 --- a/tests/testthat/gradient_golden.tsv +++ b/tests/testthat/gradient_golden.tsv @@ -1,21 +1,21 @@ case status method par A gc psi_stem collar profit -interior-1layer interior ift vcmax_25 0x1.571229588ededp-6 0x1.6274af94ca893p-15 0x1.2fe5c0bf310c1p-8 0x1.08c4016e43038p-9 0x1.591e0f15776abp-7 -interior-1layer interior ift stem_b 0x1.6c586ae568a17p+1 0x1.7ab1f9ae0843ep-7 0x1.d9c2e95fe3f7cp-1 0x1.1addc91ff05dbp-1 0x1.6b78ea6c0d439p+1 +interior-1layer interior ift vcmax_25 0x1.5742aa6ad7d32p-6 0x1.62a615f54152fp-15 0x1.3003d5c21e4b1p-8 0x1.08d62b83300b3p-9 0x1.5954ec29d4cp-7 +interior-1layer interior ift stem_b 0x1.6c6c7c8877101p+1 0x1.7ac8432c9d409p-7 0x1.d9bcceaf52aeap-1 0x1.1ada6a89a0ec3p-1 0x1.6b8e90b9a0c1cp+1 interior-1layer interior ift psi_crit 0x0p+0 0x0p+0 0x0p+0 0x0p+0 0x0p+0 -interior-1layer interior ift R_d_25 -0x1.fd6884dd6bb5cp-3 -0x1.90de3942ae2a2p-12 -0x1.57b08cc4acd79p-5 -0x1.2b6f157edb205p-6 -0x1.3c91bb0a2328ep-3 -interior-5layer interior ift vcmax_25 0x1.a789fd290384bp-5 0x1.f668e2e574766p-16 0x1.4bbb5925eeea1p-10 0x1.961814391f031p-11 0x1.91a4ee5773855p-5 -interior-5layer interior ift stem_b 0x1.bf615f4829058p+0 0x1.40cec78139b5ep-6 0x1.35865420dbf08p-1 0x1.03506a08d48c9p-1 0x1.203ce9b98f8e7p+1 +interior-1layer interior ift R_d_25 -0x1.fcec636d56075p-3 -0x1.912c0a4abe49ep-12 -0x1.57e562b17f1e2p-5 -0x1.2b94044bbc887p-6 -0x1.3bf335f656c8ep-3 +interior-5layer interior ift vcmax_25 0x1.a77e1ddad01e8p-5 0x1.f51cbe1b84e8dp-16 0x1.4ac52a921e5abp-10 0x1.94eed311eb80fp-11 0x1.91a97f341e955p-5 +interior-5layer interior ift stem_b 0x1.bf48d3044754fp+0 0x1.40da06518e92p-6 0x1.35781a72a23a4p-1 0x1.0347106fb9fcfp-1 0x1.20357c9c37cb5p+1 interior-5layer interior ift psi_crit 0x0p+0 0x0p+0 0x0p+0 0x0p+0 0x0p+0 -interior-5layer interior ift R_d_25 -0x1.53043be8d0403p-1 -0x1.75c8e3d032936p-10 -0x1.ed9b34369212dp-5 -0x1.2e209f6d45bf7p-5 -0x1.11dbf1760390ep-1 -pinned-dry-3layer pinned fd vcmax_25 0x1.1f8090c546755p-6 0x0p+0 0x0p+0 0x0p+0 0x1.1f8090c546755p-6 -pinned-dry-3layer pinned fd stem_b 0x1.2ccb4c90dc4dbp+2 0x1.64b64bc0c6a94p-6 0x1.33f595ef01ba9p-14 0x1.c3ef65a37fee1p-2 0x1.750f765efe97fp+2 -pinned-dry-3layer pinned fd psi_crit 0x1.41dadea706331p+0 0x1.7db02a6101999p-8 0x1.fff9999abeb8dp-1 0x1.e3a34a3631684p-4 0x1.03cb5d5f9853p-1 -pinned-dry-3layer pinned fd R_d_25 -0x1.b3f6e5271da55p-3 0x0p+0 0x0p+0 0x0p+0 -0x1.b3f6e5271da55p-3 +interior-5layer interior ift R_d_25 -0x1.531149ca8ab8ep-1 -0x1.75e758dd400cep-10 -0x1.ed9b5240ae8a8p-5 -0x1.2e23c35b13ce1p-5 -0x1.11e98c668492bp-1 +pinned-dry-3layer pinned fd vcmax_25 0x1.1f9eedc33dcp-6 0x0p+0 0x0p+0 0x0p+0 0x1.1f9eedc33dcp-6 +pinned-dry-3layer pinned fd stem_b 0x1.2cd6979a2aa6ep+2 0x1.64cfa2445b358p-6 0x1.33f595ef01ba9p-14 0x1.c3ef65a37fee1p-2 0x1.751ac1684cf12p+2 +pinned-dry-3layer pinned fd psi_crit 0x1.41e6f42449bap+0 0x1.7dcb470fa08b6p-8 0x1.fff9999abeb8dp-1 0x1.e3a34a3631684p-4 0x1.03e3885a1f60ep-1 +pinned-dry-3layer pinned fd R_d_25 -0x1.b4147d1197572p-3 0x0p+0 0x0p+0 0x0p+0 -0x1.b4147d1197572p-3 shutdown-1layer no-gradient fd vcmax_25 0x0p+0 0x0p+0 0x0p+0 0x0p+0 0x0p+0 shutdown-1layer no-gradient fd stem_b 0x0p+0 0x0p+0 0x0p+0 0x0p+0 0x1.21143bf2a3122p+0 shutdown-1layer no-gradient fd psi_crit 0x0p+0 0x0p+0 0x1.000000001aa4dp+0 0x1.000000001aa4dp+0 -0x1.7fef216dfc87fp-1 shutdown-1layer no-gradient fd R_d_25 -0x1.ffffffff73c8bp-1 0x0p+0 0x0p+0 0x0p+0 -0x1.00000000636f2p+0 -single-potential interior ift vcmax_25 0x1.8dbb95cac64fap-11 0x1.8665f5bea96b1p-20 0x1.0f2ea751e24e4p-11 0x1.f6f5831665267p-12 0x1.222aee3811555p-12 -single-potential interior ift leaf_specific_conductance_max 0x1.61e2e114d937p+11 0x1.116a88c064603p+3 0x1.c71412d33b7c3p+10 0x1.603f57582040fp+11 0x1.1bcb9e3c8e01bp+10 -single-potential interior ift resistance -0x1.f8de901a39b04p-14 -0x1.861138f9d9d54p-22 -0x1.34162db351084p-14 -0x1.0ed249fcfd7b3p-14 -0x1.b3ad2cf0f8p-15 -single-potential interior ift R_d_25 -0x1.090f45bc0130ep-5 -0x1.d8fdb5440484dp-15 -0x1.488dba9fc5d62p-6 -0x1.30aebe3bf1fe9p-6 -0x1.c00a35719fe39p-7 +single-potential interior ift vcmax_25 0x1.8e07cb5a9f0c2p-11 0x1.86ae3a8afb4a7p-20 0x1.0f4e264137321p-11 0x1.f72ed78c076bbp-12 0x1.22681d3500aabp-12 +single-potential interior ift leaf_specific_conductance_max 0x1.6216b907e4b84p+11 0x1.1193d5fc2142bp+3 0x1.c7319406e34f1p+10 0x1.605b83227f441p+11 0x1.1bfc831d2a5f4p+10 +single-potential interior ift resistance -0x1.f91de4957db12p-14 -0x1.8643ee01d2cdcp-22 -0x1.3420e0ff4abb9p-14 -0x1.0eda0565667bep-14 -0x1.b3f2ee785p-15 +single-potential interior ift R_d_25 -0x1.0932b4a21b5c2p-5 -0x1.d9341bd95573bp-15 -0x1.489cdcc0e300cp-6 -0x1.30bc1ea850aafp-6 -0x1.c05451eef4472p-7 diff --git a/tests/testthat/test-golden.R b/tests/testthat/test-golden.R index 7dccb63..324ddee 100644 --- a/tests/testthat/test-golden.R +++ b/tests/testthat/test-golden.R @@ -62,29 +62,29 @@ golden_rows <- list( list( inputs = list(psi_soil = 0.5, ppfd = 1500, vpd = 0.5, layers = 1L), expected = list( - psi_stem = "0x1.70a14c7893a68p+1", - opt_root_psi = "0x1.0671f2de624bep+1", - ci = "0x1.9f448245054c6p+4", - assim = "0x1.2157d30459d3ap+4", - transpiration = "0x1.4504d2a133518p-16", - gc = "0x1.0b1ba25cac3c1p-3", - profit = "0x1.0790ff442a384p+4", - e_up = "0x1.4504d35b65acfp-16", - uptake = "0x1.19e645c6a3929p-10" + psi_stem = "0x1.709c081328cc2p+1", + opt_root_psi = "0x1.066f367df1809p+1", + ci = "0x1.9f4d94a46507cp+4", + assim = "0x1.215cb3277c68cp+4", + transpiration = "0x1.450056425b687p-16", + gc = "0x1.0b2aeb7aea326p-3", + profit = "0x1.07970c77e0c6cp+4", + e_up = "0x1.450056ffb743bp-16", + uptake = "0x1.19e261c46cdc1p-10" ) ), list( inputs = list(psi_soil = 2.0, ppfd = 900, vpd = 2.0, layers = 3L), expected = list( - psi_stem = "0x1.b1b38a3125b53p+1", - opt_root_psi = "0x1.8211ae5c473bap+1", - ci = "0x1.0ddbcc40f5572p+3", - assim = "0x1.b2abf3fc8af1bp+1", - transpiration = "0x1.b282b1733fcb7p-18", - gc = "0x1.651739b6d3cecp-7", - profit = "0x1.8a0d7bc52574p-1", - e_up = "0x1.b282b4820ff91p-18", - uptake = "0x1.78dd817d62314p-12" + psi_stem = "0x1.b1bde83d4fd06p+1", + opt_root_psi = "0x1.8217d4b43c8dap+1", + ci = "0x1.0de738d727e36p+3", + assim = "0x1.b2de91f13cc6bp+1", + transpiration = "0x1.b29b56450f3c6p-18", + gc = "0x1.6544d94906decp-7", + profit = "0x1.8a7e0f7ece124p-1", + e_up = "0x1.b29b597525db4p-18", + uptake = "0x1.78f2e172d2649p-12" ) ), list( @@ -92,11 +92,11 @@ golden_rows <- list( expected = list( psi_stem = "0x1.77b2b5b35503dp+2", opt_root_psi = "0x1.37e82d8840f02p+2", - ci = "0x1.0bcf9df50cef4p+3", - assim = "0x1.9d87d266adc85p+1", + ci = "0x1.0bd5e8671ee81p+3", + assim = "0x1.9da29ffb2c45dp+1", transpiration = "0x1.9c8a7e611d793p-19", - gc = "0x1.5309210f0cc77p-7", - profit = "-0x1.db608932666c9p+1", + gc = "0x1.532136245deedp-7", + profit = "-0x1.db45bb9de7ef1p+1", e_up = "0x1.9c8a84340bf42p-19", uptake = "0x1.65cf766e154f5p-13" ) diff --git a/tests/testthat/test-gradient.R b/tests/testthat/test-gradient.R index 940ed44..8aee964 100644 --- a/tests/testthat/test-gradient.R +++ b/tests/testthat/test-gradient.R @@ -93,7 +93,9 @@ test_that("the composite reproduces the arbitrated reference gradients", { g <- grid_gradient(2.0, pars = rownames(ref)) expect_identical(g$status, "interior") expect_identical(g$method, "ift") - expect_equal(g$H, -8.9561, tolerance = 1e-4) + # -8.9561 until #51 unified the kg <-> mol water constants; the move is 1.86e-04, + # which is the 2.77e-04 change in `kg_to_mol_h2o` propagating into the Hessian. + expect_equal(g$H, -8.9578, tolerance = 1e-4) expect_equal(g$gradient[rownames(ref), "collar"], ref[, "collar"], tolerance = 5e-3) @@ -561,16 +563,36 @@ test_that("profit's gradient is the direct term alone at an interior optimum", { # this a test rather than a formality. The assignment only matters where the term # it removes is big enough to see, and that term is NOISE rather than an h^2 # truncation: `profit` is the maximum, so it is flat, and a central difference - # of it divides the solve's ~1e-9 floor by a ~1e-6 step. `?leaf_gradient` has - # the distribution over the golden grid's 136 interior rows; what matters here - # is that `psi_soil = 0.5, vpd = 2, 3 layers` is the WORST of them at 8.0e-05, - # so a tolerance three orders inside that fails if the assignment is removed. - # At the suite's usual `grid_drivers(2.0)` the same term is 2.9e-10 and this - # test would pass either way, which is the version of it written first. + # of it divides the solve's ~1e-9 floor by a ~1e-6 step. So the point has to be + # one where that noise is LARGE; at the suite's usual `grid_drivers(2.0)` the same + # term is ~1e-10 and this test would pass either way, which is the version of it + # written first. + # + # ⚠️ AND THE CHOICE DOES NOT SURVIVE A RESULTS CHANGE, which is the part that was + # not known when this was written. It pinned `psi_soil = 0.5, vpd = 2, 3 layers`, + # the worst of the interior rows at 8.0e-05. #51 moved the numbers by 2.8e-04 and + # that point's noise collapsed to 1.5e-09 — a ratio of 24 between the two + # instruments, where the test needs orders — so the test stopped demonstrating its + # own claim and failed on the `fd` side rather than the `exact` side. + # + # It is now `psi_soil = 1.0, ppfd = 1500, vpd = 1.0, 1 layer`, the worst of the + # 198 interior rows: `exact` 7.8e-16 against `fd` 2.7e-04, a ratio of **3.5e+11** + # and a stronger demonstration than the point it replaces. + # + # ⚠️ SO RE-DERIVE THE POINT, do not adjust the bounds, whenever this fails on the + # `fd` assertion. Sweep the interior rows and take the largest |fd|: + # + # for each (psi_soil, ppfd, vpd, layers) in the golden grid: + # g <- leaf_gradient(..., pars = "vcmax_25"); keep if g$status == "interior" + # solve, then fd <- central difference of profit_ in the collar at psi* + # pick argmax |fd| + # + # A failure here saying `abs(fd) <= 1e-5` means the point went quiet, NOT that the + # feature broke. A failure on `abs(exact)` is the real signal. # # ⚠️ Those figures are macOS/arm64's, and the second half of this test says why # that matters. Read it before adding an assertion on a magnitude here. - d <- grid_drivers(0.5, vpd = 2.0, layers = 3L) + d <- grid_drivers(1.0, ppfd = 1500, vpd = 1.0, layers = 1L) g <- do.call(leaf_gradient, c(d, list(pars = "vcmax_25"))) expect_identical(g$status, "interior") @@ -633,9 +655,11 @@ test_that("profit's gradient is the direct term alone at an interior optimum", { # 1e-12 was pinning a landing point, and this package's own guide names ~1e-9 as # the floor, so that is what the bound should have been all along. # - # What carries the test is the GAP, not either bound: measured here, `exact` - # 1.2e-10 against `fd` 2.1e-04 is a factor of 1.7e+06. Both bounds sit three or - # more orders inside that, so removing the assignment still fails this. + # What carries the test is the GAP, not either bound: at the re-derived point + # (see above) `exact` is 7.8e-16 against `fd` 2.7e-04, a factor of **3.5e+11**. + # Both bounds sit orders inside that, so removing the assignment still fails this. + # At the point this pinned before #51 the gap was 1.7e+06, itself ample; the + # margin is not the fragile part, the choice of point is. expect_lt(abs(exact), 1e-9) expect_gt(abs(fd), 1e-5) }) From 014ac414273e652bca49fa931b021cdadfe7c711 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 20 Aug 2026 09:00:12 +1000 Subject: [PATCH 2/3] Update the CI consumer's two pinned values The inline consumer program in cpp-tests.yml asserts a profit and a gradient at fixed operating points, and #51 moved both: profit by 5.2e-04 against a 1e-6 tolerance, and dA/dvcmax_25 by 1.61e-05 against 1e-5. Two of the three C++ jobs went red while `make -C tests/cpp`, `make -C tests/cpp bench` and `make test-cmake` were all green locally -- which is the hazard the guide records about this heredoc. Both values now name the file to copy them from, and say what moved them. Verified by extracting the two heredocs by line range and building the consumer against a locally installed prefix, which is the only way to exercise it outside CI: exit 0. Co-Authored-By: Claude Opus 5 (1M context) --- .github/workflows/cpp-tests.yml | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cpp-tests.yml b/.github/workflows/cpp-tests.yml index b01b89b..70b6161 100644 --- a/.github/workflows/cpp-tests.yml +++ b/.github/workflows/cpp-tests.yml @@ -219,8 +219,13 @@ jobs: return 1; } // 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] - 0.0209349) > 1e-5) { + // compared for the same reason profit is below. ⚠️ THIS MOVES WITH THE + // MODEL and nothing local builds this file: #92 took it from 0.0209349 + // to 0.0209394 (inside the 1e-5) and #51 to 0.0209510 (outside it, by + // 1.61e-05). It is the `interior-1layer` / `vcmax_25` / `A` cell of + // tests/testthat/gradient_golden.tsv -- read it from there, do not + // re-derive it. + if (std::fabs(g[0].grad[0] - 0.0209510) > 1e-5) { return 1; } l.set_physiology(roots, 900, {2.0}, soil_depth, @@ -235,7 +240,15 @@ jobs: // tolerances. (The value here read 2.5158434693939866 until #33, which // is 2.2e-08 off the golden row and inside the tolerance, so it never // failed; corrected so it cannot be mistaken for the golden value.) - return std::fabs(l.profit_ - 2.5158434915102319) < 1e-6 ? 0 : 1; + // + // ⚠️ COPY THIS FROM THE GOLDEN FILE WHENEVER RESULTS MOVE. It was + // 2.5158434915102319 until #51 unified the water molar mass, which moved + // it by 5.2e-04 -- 500x the 1e-6 tolerance -- and took two of the three + // C++ jobs red. Neither `make -C tests/cpp` nor `make test-cmake` builds + // this program, so a local run is green while CI is not: that is the + // hazard the developer guide records about this heredoc, and a + // results-moving PR has to come here on purpose. + return std::fabs(l.profit_ - 2.517156924533102) < 1e-6 ? 0 : 1; } EOF cmake -B build \ From e8380d630f7856ff662d797f12eac139a4fdb356 Mon Sep 17 00:00:00 2001 From: Daniel Falster Date: Thu, 20 Aug 2026 09:57:13 +1000 Subject: [PATCH 3/3] Cut the change history out of the comments Review feedback: comments should carry only what has enduring forward value -- the contract, the invariant, the hazard a future editor could reintroduce -- not an account of what the values used to be or how far they moved. That belongs in the PR body, the first PR comment and NEWS.md, all of which already have it. Net -74 lines across five files. What survives is phrased as a rule: "both directions derive from this, do not reintroduce a second literal", "copy this value from the golden file when results move -- no local build compiles this program", "re-derive the operating point rather than adjusting the bounds". Co-Authored-By: Claude Opus 5 (1M context) --- .github/workflows/cpp-tests.yml | 19 +++++--------- inst/include/phylloptim/constants.hpp | 32 +++-------------------- tests/cpp/test_leaf.cpp | 36 ++++++-------------------- tests/testthat/test-gradient.R | 37 +++++++-------------------- tests/testthat/test-surface.R | 10 +++----- 5 files changed, 30 insertions(+), 104 deletions(-) diff --git a/.github/workflows/cpp-tests.yml b/.github/workflows/cpp-tests.yml index 70b6161..e0052a9 100644 --- a/.github/workflows/cpp-tests.yml +++ b/.github/workflows/cpp-tests.yml @@ -219,12 +219,9 @@ jobs: return 1; } // The R layer's arbitrated reference for this operating point, loosely - // compared for the same reason profit is below. ⚠️ THIS MOVES WITH THE - // MODEL and nothing local builds this file: #92 took it from 0.0209349 - // to 0.0209394 (inside the 1e-5) and #51 to 0.0209510 (outside it, by - // 1.61e-05). It is the `interior-1layer` / `vcmax_25` / `A` cell of - // tests/testthat/gradient_golden.tsv -- read it from there, do not - // re-derive it. + // compared for the same reason profit is below. ⚠️ COPY THIS FROM + // tests/testthat/gradient_golden.tsv WHENEVER RESULTS MOVE -- the + // `interior-1layer` / `vcmax_25` / `A` cell. Do not re-derive it. if (std::fabs(g[0].grad[0] - 0.0209510) > 1e-5) { return 1; } @@ -241,13 +238,9 @@ jobs: // is 2.2e-08 off the golden row and inside the tolerance, so it never // failed; corrected so it cannot be mistaken for the golden value.) // - // ⚠️ COPY THIS FROM THE GOLDEN FILE WHENEVER RESULTS MOVE. It was - // 2.5158434915102319 until #51 unified the water molar mass, which moved - // it by 5.2e-04 -- 500x the 1e-6 tolerance -- and took two of the three - // C++ jobs red. Neither `make -C tests/cpp` nor `make test-cmake` builds - // this program, so a local run is green while CI is not: that is the - // hazard the developer guide records about this heredoc, and a - // results-moving PR has to come here on purpose. + // ⚠️ COPY THIS FROM THE GOLDEN FILE WHENEVER RESULTS MOVE -- it is the + // psi_soil=2, ppfd=900, vpd=2, T=25, layers=1 row. No local build + // compiles this program, so forgetting it is green locally and red in CI. return std::fabs(l.profit_ - 2.517156924533102) < 1e-6 ? 0 : 1; } EOF diff --git a/inst/include/phylloptim/constants.hpp b/inst/include/phylloptim/constants.hpp index 99033ef..f436653 100644 --- a/inst/include/phylloptim/constants.hpp +++ b/inst/include/phylloptim/constants.hpp @@ -56,35 +56,11 @@ inline constexpr double ko_ha = 36.38e3; // Leaf::umol_per_mol_to_Pa_, derived from atm_kpa_. The old `0.1013` was 101.3 // kPa hard-coded; don't reinstate it. -// The molar mass of water, and the ONE place it is written down (#51). Everything -// that crosses between a kg basis and a mol basis is derived from this, so the two -// directions are reciprocal by construction and a round trip is the identity to -// within one rounding. +// The molar mass of water -- 18.015 g/mol, from the standard atomic weights -- and +// the ONE place it is written down. Both conversion directions derive from it, so +// they are reciprocal by construction; do not reintroduce a second literal (#51). // -// ⚠️ THIS USED TO BE TWO INDEPENDENT NUMBERS THAT DISAGREED BY 0.0277%, and the -// header said so on purpose: `kg_to_mol_h2o` was 55.4939 while `kg_per_mol_h2o` was -// 0.018015, with a comment recording that the first was "intentionally distinct -// from 1/kg_to_mol_h2o ... kept at the historical 0.018015 to preserve results". -// Two constants naming the same physical quantity in opposite directions, used in -// opposite halves of the model: the demand side converted transpiration kg -> mol -// with the first, the supply side converted uptake mol -> kg with the second. -// -// WHICH ONE WAS WRONG IS NOT A MATTER OF CONVENTION, which is what let this be -// settled rather than argued. 55.4939 is 1/0.018020, i.e. it encodes a molar mass of -// 18.0200 g/mol. The molar mass of water is 18.015 g/mol -- from the standard atomic -// weights, 2(1.008) + 15.999 -- so 0.018015 is the physical value and the forward -// constant was the odd one. Unifying therefore moves `kg_to_mol_h2o` from 55.4939 to -// 55.509298..., which is the LARGER of the two possible moves, and it is still the -// right one: the alternative preserves more digits by adopting a molar mass water -// does not have. -// -// It also happens to leave plant's `using ::phylloptim::kg_per_mol_h2o` -- -// tf24_strategy.cpp's water consumption rate, the only live use of either name over -// there -- multiplying by an unchanged constant. That is a convenience, not the -// reason; plant's results still move, because the leaf's operating point does. -// -// Both old names are kept, and deliberately: plant `using`-declares both, so -// deleting either would break its build for no benefit. +// Both names below are kept because plant `using`-declares both. inline constexpr double molar_mass_h2o = 0.018015; // kg mol^-1 // kg mol^-1, for converting a molar water flux back to kg. inline constexpr double kg_per_mol_h2o = molar_mass_h2o; diff --git a/tests/cpp/test_leaf.cpp b/tests/cpp/test_leaf.cpp index b471a90..3f6c27c 100644 --- a/tests/cpp/test_leaf.cpp +++ b/tests/cpp/test_leaf.cpp @@ -274,20 +274,8 @@ void test_solve_single_layer() { ok(l.opt_psi_stem_ <= l.psi_crit, "stem stays within psi_crit"); ok(l.transpiration_ > 0.0, "transpiration is positive"); ok(l.assim_colimited_ > 0.0, "assimilation is positive"); - // Regression guards -- see the note at the top of this file. Moved twice: - // - // PLAN 11a, the collar root-find: opt_psi_stem_ 3.595247 -> 3.595088 and - // assim_colimited_ 5.599511 -> 5.599153, both ~1e-4 relative, which is the - // argmax correction and not rounding. profit_ and transpiration_ did not move - // at this tolerance -- profit_ because it is the maximum and therefore flat. - // - // #51, unifying the kg <-> mol water constants on the molar mass of water: - // opt_psi_stem_ -> 3.595332, assim_colimited_ -> 5.601016, profit_ 2.515843 -> - // 2.517157. The forward constant rose 0.0277%, so conductance-per-unit- - // transpiration rose with it, and the leaf buys more carbon for the same water. - // ⚠️ profit_ DID move this time, by 5.2e-04, which is the largest of the three: - // the flat-maximum argument protects the maximum against a displacement of its - // LOCATION, not against the objective itself being rescaled. + // Regression guards -- see the note at the top of this file. Regenerate these + // deliberately, alongside the golden file, and state the movement in the PR. near(l.opt_psi_stem_, 3.595332, 1e-5, "opt_psi_stem_"); near(l.assim_colimited_, 5.601016, 1e-5, "assim_colimited_"); near(l.transpiration_, 1.141941e-05, 1e-5, "transpiration_"); @@ -2487,14 +2475,9 @@ bool mentions(const std::string& haystack, const char* needle) { // last knot for years: the shortfall is invisible from outside unless the domain // edge is compared with the function that is supposed to define it. // The kg <-> mol water conversions are reciprocal, and the round trip is the -// identity (#51). They used to be two independently written numbers disagreeing by -// 0.0277%, used in opposite halves of the model -- the demand side converting -// transpiration kg -> mol, the supply side converting uptake mol -> kg -- so a flux -// pushed through both did not come back. -// -// Asserted rather than left to the header comment, because "these two constants are -// reciprocals" is exactly the kind of claim that was already written down here and -// was false. +// identity (#51). Asserted rather than documented: the demand side converts +// transpiration kg -> mol and the supply side converts uptake mol -> kg, so a +// second literal anywhere breaks the round trip silently. void test_water_mass_conversions_are_reciprocal() { printf("kg <-> mol water conversions\n"); // Exact to the last bit in one direction: kg_to_mol_h2o IS 1/molar_mass_h2o. @@ -2505,7 +2488,7 @@ void test_water_mass_conversions_are_reciprocal() { // The round trip cannot be bit-exact -- 1/x then *x is not the identity for most // x -- so the claim is that it is within one rounding, which is what "reciprocal" - // can actually buy. Before #51 this was out by 2.8e-04. + // can actually buy. for (double kg : {1e-9, 1e-6, 1e-3, 1.0, 1e3}) { const double round_trip = kg * phylloptim::kg_to_mol_h2o * phylloptim::kg_per_mol_h2o; @@ -2514,13 +2497,10 @@ void test_water_mass_conversions_are_reciprocal() { phylloptim::util::format_double(kg)); } - // And the value is the molar mass of water, not a neighbouring one: 18.015 g/mol - // from the standard atomic weights, 2(1.008) + 15.999. The pre-#51 forward - // constant implied 18.0200, which is what this pins against. + // The value is water's molar mass, not a neighbouring one: 18.015 g/mol from the + // standard atomic weights, 2(1.008) + 15.999. near(phylloptim::molar_mass_h2o * 1000.0, 18.015, 1e-9, "the molar mass is water's, in g/mol"); - ok(std::abs(phylloptim::kg_to_mol_h2o - 55.4939) > 1e-3, - "the forward constant is no longer the pre-#51 55.4939"); } void test_knot_grid_reaches_its_intended_domain() { diff --git a/tests/testthat/test-gradient.R b/tests/testthat/test-gradient.R index 8aee964..1dddbeb 100644 --- a/tests/testthat/test-gradient.R +++ b/tests/testthat/test-gradient.R @@ -93,8 +93,6 @@ test_that("the composite reproduces the arbitrated reference gradients", { g <- grid_gradient(2.0, pars = rownames(ref)) expect_identical(g$status, "interior") expect_identical(g$method, "ift") - # -8.9561 until #51 unified the kg <-> mol water constants; the move is 1.86e-04, - # which is the 2.77e-04 change in `kg_to_mol_h2o` propagating into the Hessian. expect_equal(g$H, -8.9578, tolerance = 1e-4) expect_equal(g$gradient[rownames(ref), "collar"], ref[, "collar"], @@ -568,26 +566,16 @@ test_that("profit's gradient is the direct term alone at an interior optimum", { # term is ~1e-10 and this test would pass either way, which is the version of it # written first. # - # ⚠️ AND THE CHOICE DOES NOT SURVIVE A RESULTS CHANGE, which is the part that was - # not known when this was written. It pinned `psi_soil = 0.5, vpd = 2, 3 layers`, - # the worst of the interior rows at 8.0e-05. #51 moved the numbers by 2.8e-04 and - # that point's noise collapsed to 1.5e-09 — a ratio of 24 between the two - # instruments, where the test needs orders — so the test stopped demonstrating its - # own claim and failed on the `fd` side rather than the `exact` side. - # - # It is now `psi_soil = 1.0, ppfd = 1500, vpd = 1.0, 1 layer`, the worst of the - # 198 interior rows: `exact` 7.8e-16 against `fd` 2.7e-04, a ratio of **3.5e+11** - # and a stronger demonstration than the point it replaces. - # - # ⚠️ SO RE-DERIVE THE POINT, do not adjust the bounds, whenever this fails on the - # `fd` assertion. Sweep the interior rows and take the largest |fd|: + # ⚠️ THE POINT DOES NOT SURVIVE A RESULTS CHANGE, so RE-DERIVE IT rather than + # adjusting the bounds whenever this fails on the `fd` assertion: sweep the golden + # grid's interior rows and take the largest |fd|. # # for each (psi_soil, ppfd, vpd, layers) in the golden grid: # g <- leaf_gradient(..., pars = "vcmax_25"); keep if g$status == "interior" # solve, then fd <- central difference of profit_ in the collar at psi* # pick argmax |fd| # - # A failure here saying `abs(fd) <= 1e-5` means the point went quiet, NOT that the + # A failure saying `abs(fd) <= 1e-5` means the point went quiet, NOT that the # feature broke. A failure on `abs(exact)` is the real signal. # # ⚠️ Those figures are macOS/arm64's, and the second half of this test says why @@ -647,19 +635,12 @@ test_that("profit's gradient is the direct term alone at an interior optimum", { # between "the dropped term is small" and "the dropped term is unmeasurable by # the route that would have supplied it". # - # ⚠️ THE BOUND ON `exact` IS THE SOLVER FLOOR, NOT 1e-12, and it was 1e-12 here - # for one commit's worth of luck. #92's knot grid moved where the collar - # root-find lands inside its own tolerance, and `exact` went from 2.4e-15 to - # 1.2e-10 on this platform without anything about the answer changing -- which is - # precisely the mechanism the note above describes for Linux, arriving on macOS. - # 1e-12 was pinning a landing point, and this package's own guide names ~1e-9 as - # the floor, so that is what the bound should have been all along. + # ⚠️ THE BOUND ON `exact` IS THE SOLVER FLOOR (~1e-9), not a landing point. Pinning + # it tighter pins which side of its own tolerance the collar root-find lands on, + # which moves for reasons unrelated to this feature. # - # What carries the test is the GAP, not either bound: at the re-derived point - # (see above) `exact` is 7.8e-16 against `fd` 2.7e-04, a factor of **3.5e+11**. - # Both bounds sit orders inside that, so removing the assignment still fails this. - # At the point this pinned before #51 the gap was 1.7e+06, itself ample; the - # margin is not the fragile part, the choice of point is. + # What carries the test is the GAP, not either bound: `exact` 7.8e-16 against `fd` + # 2.7e-04 is a factor of 3.5e+11, so both bounds sit orders inside it. expect_lt(abs(exact), 1e-9) expect_gt(abs(fd), 1e-5) }) diff --git a/tests/testthat/test-surface.R b/tests/testthat/test-surface.R index afe990c..6fc9e69 100644 --- a/tests/testthat/test-surface.R +++ b/tests/testthat/test-surface.R @@ -94,13 +94,9 @@ test_that("a non-default trait reaches the model through leaf_model()", { traits = leaf_traits(vcmax_25 = 150)) expect_gt(hi_vcmax$A, base$A) - # ⚠️ `psi_crit` MOVES WITH `stem_b` HERE, and it has to. This case used to pass - # `stem_b = 2.0` alone, leaving the default `psi_crit` of 5.870283 -- which at - # that stem_b is past the curve's own P99 of 3.5359, i.e. a combination the model - # cannot evaluate. It went unnoticed because nothing here solved: the constructor - # did not check it and `proportion_of_conductivity` is a closed form that never - # reads the spline. #38's check refuses it now, so the trait pair moves together, - # and 3.0 is roughly the P95 that stem_b implies (3.0118). + # ⚠️ `psi_crit` MOVES WITH `stem_b`, and it has to: at stem_b = 2.0 the curve's P99 + # is 3.5359, so the default psi_crit of 5.870283 is off the end of it and #38's + # check refuses the pair. 3.0 is roughly the P95 that stem_b implies (3.0118). brittle <- leaf_model(leaf_traits(stem_b = 2.0, psi_crit = 3.0)) expect_lt(brittle$proportion_of_conductivity(2.0), leaf_model()$proportion_of_conductivity(2.0))