ECCO-Darwin parameter inventory (Carroll 2020 build)¶

A verified count of biogeochemistry parameters in the ECCO-Darwin v04 LLC270 JAMES paper configuration (Carroll et al. 2020, Darwin 1). Captured here so DarwinDiff scoping arguments rest on real numbers rather than estimates.

Note (2026-05-09): Carroll 2022 (v05, Darwin 3) inherits Carroll 2020's six calibrated values bit-for-bit — verified directly by reading v04/llc270_JAMES_paper/code_darwin/{darwin_init_fixed.F, darwin_generate_phyto.F} and v05/llc270/input/data.darwin. The numbers in this doc are therefore current for both Carroll 2020 and Carroll 2022 setups. The DarwinDiff project's active recovery target is Carroll 2022 / v05 (publicly-accessible), but the underlying parameter inventory is unchanged. See docs/findings/2026_05_09.md finding 8 and docs/research_log.md §F1.

Method¶

Read three files line-by-line from a fresh clone of MITgcm-contrib/ecco_darwin at master, scoped to v04/llc270_JAMES_paper/code_darwin/:

DARWIN_OPTIONS.h (111 lines), to determine which #ifdef blocks are active in the compiled binary.
darwin_init_fixed.F (390 lines), with every parameter assignment classified.
darwin_generate_phyto.F (782 lines), grep-confirmed as mostly mechanical derivation from the init_fixed.F scalars.
darwin_plankton.F (1711 lines), the dynamics integrator. It uses parameters defined elsewhere; no new independent parameters introduced.

Active compile-time flags (Carroll 2020 build)¶

From DARWIN_OPTIONS.h:

Active: ALLOW_CARBON, GEIDER, DYNAMIC_CHL, MINFE, IRON_SED_SOURCE, IRON_SED_SOURCE_VARIABLE, PART_SCAV, NINE_SPECIES_SETUP, TEMP_VERSION 2, USE_QSW, USE_EXFWIND, USE_EXFCO2, PORT_RAND, CALC_RATE_TOTALS
Inactive: WAVEBANDS, OASIM, OLD_GRAZE, ALLOW_DIAZ, ALLOW_DENIT, ALLOW_MUTANTS, all DAR_DIAG_*, RELAX_NUTS, FLUX_NUTS

Denitrification, diazotrophy, spectral radiative transfer, and most diagnostics are not in the compiled binary for this run.

Model dimensions (`DARWIN_SIZE.h`)¶

5 phytoplankton functional types (npmax = 5; the NINE_SPECIES_SETUP flag name is historical)
2 zooplankton functional types (nzmax = 2)
4 elemental components per zooplankton (nCompZooMax = 4: P, N, Fe, Si)
39 prognostic tracers total, matching Carroll 2020 §2.3

Verified parameter counts¶

Class	Count	Source file
Independent active tunable scalars	103	`darwin_init_fixed.F`
Derived equalities (`Kpremin_N = Kpremin_P`, `wn_sink = wp_sink`, etc.)	6	`darwin_init_fixed.F`
Dead in this build (#ifdef inactive: denit, diaz, mutants, diagnostics)	11	`darwin_init_fixed.F`
Unit conversions (`parconv`, `permil`, `Pa2Atm`)	3	`darwin_init_fixed.F`
Hardcoded per-phyto identity traits (`physize`, `phyto_esd`, `phyto_vol`, `diacoc`, `diazotroph`, `nsource`, `ap_type` × 5 types)	35 (7 traits × 5 phyto types, exact)	`darwin_generate_phyto.F`
New independent parameters	0	`darwin_plankton.F`

The 35 hardcoded per-phyto traits are classifications (small vs large, diatom vs cocco vs other, etc.) that define the identity of each phytoplankton type, not adjustable knobs. The kinetic per-phyto arrays (mu, ksatPO4, R_NP, wsink, ...) are derived from the 103 init_fixed.F scalars by simple assignment or arithmetic (for example ksatNO3(np) = ksatPO4(np) * R_NP(np)).

Headline: ~103 independent tunable scalar knobs.

Parameters tuned via Green's functions in Carroll 2020¶

Six. Source values verified directly in the Carroll 2020 build, with paper Table 1 cross-reference:

#	Source variable	File:line	Optimized value	Paper Table 1 name
1	`alpfe`	`init_fixed.F:83`	0.92831	Iron dust solubility
2	`scav_rat`	`init_fixed.F:101`	10.41124 × 0.005 / 86400	Iron scavenging rate
3	`Smallgrow`	`init_fixed.F:161`	0.66098	Small phytoplankton growth rate
4	`Biggrow`	`init_fixed.F:162`	0.43148	Large phytoplankton growth rate
5	`diatomgraz`	`init_fixed.F:272`	0.83003	Diatom palatability
6	`R_PICPOC`	`generate_phyto.F:484`	0.04245	PIC/POC ratio

Each parameter has its pre-optimization default visible in a commented-out line nearby (for example cswd scav_rat=0.005 _d 0/(86400.0 _d 0) at line 99). The Green's functions workflow literally edits these constants in source and recompiles per experiment — the "labor-intensive" cycle this project replaces with autograd.

What this means for DarwinDiff¶

Calibration coverage gap: 6 / 103 ≈ 5.8 %. The other ~94 % of independently tunable knobs sit at expert or literature defaults applied uniformly across the global ocean. Many are single global scalars: Kdop = 2 / (100 × 86400) controls DOC remineralization rate everywhere on Earth, kgrazesat = 0.085 is one number for grazing half-saturation across all ocean conditions, phytoTempOptimum is one curve per phytoplankton class with no spatial variation. Replacing such scalars with MLP-predicted spatial fields, which is what DarwinDiff's parameter-learner does, is a structurally cheap upgrade per parameter that reaches well past the Green's functions ceiling of "a handful at a time."

Savelli et al. 2026 explicitly flagged the 100-day fixed DOC remineralization (Kdop in the source) as a real limitation. Other parameters in the 94 % likely sit in the same shape: known to be uncertain, plausibly important, but unreached by Green's functions because Green's functions cannot afford them.

Darwin 3 (v06/llc270) — also audited¶

Darwin 3 is the version used in the repo's v05 and v06 setups. It is a major architectural rework of Darwin 1: most parameters are now exposed via namelist files in input_darwin/ rather than hardcoded in local code_darwin/ source. The code_darwin/ directory in v06/llc270 contains only headers (DARWIN_OPTIONS.h, DARWIN_SIZE.h, etc.); the kinetic source lives upstream in MITgcm/pkg/darwin/.

Model dimensions (`v06/llc270/code_darwin/DARWIN_SIZE.h`)¶

nplank = 10 — total plankton types (was 5 phyto + 2 zoo = 7 in Darwin 1)
nGroup = 7 — functional groups: PicoCyano, PicoEuk, Cocco, Diazo, Diatom, Dino, Zoo
nPhoto = 6 — phototroph types
nopt = 12 — optical types
nlam = 1 — wavebands (RADTRANS not active in this build)

Active compile-time flags¶

From v06/llc270/code_darwin/DARWIN_OPTIONS.h (174 lines):

Active (21 flags): DARWIN_ALLOW_CHLQUOTA, DARWIN_ALLOW_CDOM, DARWIN_ALLOW_CARBON, DARWIN_ALLOW_DENIT, DARWIN_BOTTOM_SINK, DARWIN_ALLOW_GEIDER, DARWIN_GEIDER_RHO_SYNTH, DARWIN_DIAG_IOP, DARWIN_TEMP_VERSION 4, DARWIN_MINFE, DARWIN_PART_SCAV, DARWIN_IRON_SED_SOURCE_VARIABLE, DARWIN_DIAG_PERTYPE, DARWIN_ALLOW_CONS, DARWIN_DIAG_TENDENCIES, DARWIN_ALLOW_RADIv2, DARWIN_NUTRIENT_RUNOFF, DARWIN_SOLVESAPHE, DARWIN_TOTALPHSCALE, DARWIN_ALLOW_HYDROTHERMAL_VENTS, DARWIN_CDOM_UNITS_CARBON
Inactive (21 flags): DARWIN_ALLOW_NQUOTA, PQUOTA, FEQUOTA, SIQUOTA, EXUDE, NITRATE_FELIMIT, AVPAR, CHL_INIT_LEGACY, SCATTER_CHL, GRAZING_SWITCH, ALLOMETRIC_PALAT, NOZOOTEMP, NOTEMP, TEMP_RANGE, IRON_SED_SOURCE_POP, DEBUG, PART_SCAV_POP, RANDOM_TRAITS, TWO_SPECIES_SETUP, NINE_SPECIES_SETUP, ALLOW_DIAZ

Notable: denitrification is on in Darwin 3 (was off in Carroll 2020), diazotrophy is still off, the Darwin 1 random-trait code path is fully replaced by the new allometric trait machinery.

Verified tunable parameter counts (from namelists)¶

Read in full: data.darwin (267 lines) and data.traits (93 lines). Each namelist counted by listing every distinct LHS name.

Namelist	Tunable parameter names	Total names	Notes
`&DARWIN_FORCING_PARAMS`	20	71	12 input scaling factors (`darwin_inscal_`) + 8 stoichiometric ratios for runoff (`R__runoff`). Excludes file paths, dates, periods, 3 boolean toggles.
`&DARWIN_INTERP_PARAMS`	0	28	Interpolation grid metadata only.
`&DARWIN_PARAMS` (kinetic core)	29	37	iron (8: `alpfe`, `freefemax`, `depthfesed`, `scav_tau`, `ligand_tot`, `scav_POC_wgt`, `scav_PSi_wgt`, `scav_PIC_wgt`), DOM remin (4: `kdoc`/`kdop`/`kdon`/`kdofe`), POM remin (5: `kPOC`/`kPOP`/`kPON`/`kPOFe`/`kPOSi`), sinking (6: `wC_sink`/`wN_sink`/`wP_sink`/`wFe_sink`/`wSi_sink`/`wPIC_sink`), plus `phygrazmin`, `hollexp`, `tempCoeffArr`, `PARmin`, `SURFDICMIN`, `SURFALKMIN`. Excludes 5 numerical-config (`darwin_chlIter0`, `darwin_pickupSuff`, `darwin_chlInitBalanced`, `darwin_seed`, `darwin_disscSelect`) and 1 dead (`diaz_ini_fac`, `ALLOW_DIAZ` undef). 2 more (`selectPHsolver`, `selectK1K2const`) are commented out.
`&DARWIN_CDOM_PARAMS`	5	5 active	`fracCDOM`, `cdomdegrd`, `CDOMbleach`, `PARCDOM`, `CDOMcoeff`. 3 more (`R_NP_CDOM`, `R_FeP_CDOM`, `R_CP_CDOM`) commented out.
`&DARWIN_RADTRANS_PARAMS`	10 (7 scalars + 3 array names)	14	scalar tunables: `darwin_Sdom`, `darwin_aCDOM_fac`, `darwin_part_size_P`, `darwin_rCDOM`, `darwin_RPOC`, `darwin_absorpSlope`, `darwin_bbbSlope`. 3 spectral arrays of 13 values each: `darwin_scatSwitchSizeLog`, `darwin_scatSlopeSmall`, `darwin_scatSlopeLarge`. Excludes 3 file paths and 1 boolean (`darwin_allomSpectra`).
`&DARWIN_RANDOM_PARAMS`	0	0	empty namelist
`&DARWIN_TRAIT_PARAMS`	28	48	excludes `grp_names` (identity), 16 group classification flags (`grp_nplank`, `grp_photo`, `grp_pred`, `grp_prey`, `grp_hasSi`, `grp_hasPIC`, `grp_DIAZO`, `grp_useNH4`, `grp_useNO2`, `grp_useNO3`, `grp_combNO`, `grp_bacttype`, `grp_aerobic`, `grp_denit`, `grp_tempMort`, `grp_tempMort2`, `grp_aptype`), and 2 boolean/select configs (`darwin_effective_ksat`, `darwin_select_kn_allom`). Most tunables are arrays at size `nGroup=7`, `nPhoto=6`, or `nplank=10`; some (e.g. `a_PCmax(1..6)`) are set per index.
`data.traits` `&DARWIN_TRAITS`	8	8	`EXPORTFRACMORT`, `EXPORTFRACMORT2`, `PALAT` (10×10 matrix), `ASSEFF` (10×10), `GRAZEMAX`, `EXPORTFRACPREYPRED` (10×10), `MORT`, `MORT2`.

Darwin 3 distinct tunable parameter names: exactly 100.

Counting basis	Count
Distinct tunable parameter names (across all namelists in `data.darwin` + `data.traits`)	100
Individual tunable values, arrays expanded over plankton, groups, and matrix dimensions	657

Breakdown of the 657 individual values:

Source	Values	How counted
`&DARWIN_FORCING_PARAMS`	20	20 scalars × 1
`&DARWIN_PARAMS`	29	29 scalars × 1
`&DARWIN_CDOM_PARAMS`	5	5 scalars × 1
`&DARWIN_RADTRANS_PARAMS`	46	7 scalars + 3 arrays × 13
`&DARWIN_TRAIT_PARAMS`	207	sum of array sizes per name (10+6+6+6+6+6+1+1+7+7+7+6+6+7+7+7+6+1+1+1+7+7+7+7+7+7+7+49)
`&DARWIN_TRAITS`	350	10+10+100+100+10+100+10+10
Total	657

Architectural difference that matters for DarwinDiff¶

Darwin 1: parameters hardcoded in source (code_darwin/); each Green's functions experiment recompiles a different binary. Tunable knobs ≈ 103 scalars in init_fixed.F.

Darwin 3: parameters exposed via namelist files (input_darwin/data.darwin, data.traits). Tunable knobs ≈ 101 distinct names at the namelist level, with most being arrays. No recompile needed to vary them.

This means Darwin 3 is structurally a better target for DarwinDiff. Spatially-varying parameter learning (the DarwinDiff approach) would write per-cell parameter fields rather than per-class scalars; the namelist-driven architecture makes it cheaper to plug in MLP-predicted values without source modifications.

Darwin 3 caveats not yet verified¶

Default values for parameters NOT explicitly overridden in v06/llc270 namelists live upstream in MITgcm/pkg/darwin/ source; that code is not in MITgcm-contrib/ecco_darwin and was not audited here. There may be additional parameters with literature defaults that the v06 setup inherits silently.
The &DARWIN_RADTRANS_PARAMS namelist is read even though the active flag set does not include ALLOW_RADTRANS per the readme. Worth checking whether those parameters affect the v06 binary or are dead.

Caveats¶

Darwin 1 numbers are exact for the Carroll 2020 build (v04/llc270_JAMES_paper). All three key source files read line-by-line.
Darwin 3 numbers are exact for the namelist content of v06/llc270 (data.darwin, data.traits). The upstream MITgcm pkg/darwin/ source (where defaults live for unset parameters) was not audited.
"Independent tunable" excludes derived equalities, dead-code parameters, unit conversions, identity classifications, file-path and date strings, and pure numerical-config parameters.
"Tunable" is partly a judgment call. Stricter or looser definitions could shift the counts by ±10–20.

Provenance¶

Audit performed 2026-05-02 via shallow clone of MITgcm-contrib/ecco_darwin (master branch).

Darwin 1 (v04/llc270_JAMES_paper/code_darwin/): DARWIN_OPTIONS.h (111 lines), DARWIN_SIZE.h (131 lines), darwin_init_fixed.F (390 lines), darwin_generate_phyto.F (782 lines) all read in full. darwin_plankton.F (1711 lines) grep-scanned for top-level assignments.
Darwin 3 (v06/llc270/): code_darwin/DARWIN_OPTIONS.h (174 lines), code_darwin/DARWIN_SIZE.h (34 lines), input_darwin/data.darwin (267 lines), input_darwin/data.traits (93 lines) all read in full.

Classifications cross-checked against DARWIN_OPTIONS.h #ifdef flags in each version. Temp clone deleted after audit; all numbers are reproducible by anyone running the same procedure.

Appendix A — Darwin 1 (`darwin_init_fixed.F`) full parameter list¶

123 distinct named parameters total. Categories below sum to that.

A.1 Independent active tunable scalars (103)

Light + attenuation (6): k0, kc, parfrac, chlpmax, chlpmin, istar

Iron cycle (11): alpfe ★, scav, ligand_tot, ligand_stab, freefemax, depthfesed, fesedflux, fesedflux_pcm, scav_rat ★, scav_inter, scav_exp

Nitrification + O₂ (4): O2crit, Knita, Knitb, PAR0

GEIDER growth scalars (4): Smallgrow ★, Biggrow ★, Smallgrowrange, Biggrowrange

GEIDER chlorophyll + quantum yield (8): smallchl2cmax, smallchl2cmaxrange, Bigchl2cmax, Bigchl2cmaxrange, smallmQyield, smallmQyieldrange, BigmQyield, BigmQyieldrange

Other phyto (2): aphy_chl_ave, inhibcoef_geid_val

Dynamic chlorophyll (1): acclimtimescl

Mortality + sinking scalars (8): Smallmort, Bigmort, Smallmortrange, Bigmortrange, Smallexport, Bigexport, SmallSink, BigSink

Temperature (8): tempcoeff1, tempcoeff2_small, tempcoeff2_big, tempcoeff3, tempmax, temprange, tempnorm, tempdecay

Phosphate half-saturation per phyto class (8): SmallPsat, BigPsat, ProcPsat, UniDzPsat, SmallPsatrange, BigPsatrange, ProcPsatrange, UniDzPsatrange

Other nutrient (8): ksatNH4fac, ksatNO2fac, sig1, sig2, sig3, ngrowfac, ilight, val_ksatsi

Elemental ratios — active (5): val_R_SiP_diatom, val_R_NP, val_RFeP, val_R_PC, val_R_PICPOC

Grazing (14): kgrazesat, phygrazmin, GrazeFast, GrazeSlow, GrazeEfflow, GrazeEffmod, GrazeEffhi, palathi, palatlo, diatomgraz ★, coccograz, olargegraz, ExGrazfracbig, ExGrazfracsmall

Zooplankton mortality + export (4): ZoomortSmall, ZoomortBig, ZooexfacSmall, ZooexfacBig

Phyto biomass threshold (1): phymin

DOM remineralisation (3): Kdop, Kdon, KdoFe

POM remineralisation + sinking, independent (3): Kpremin_P, Kpremin_Si, wp_sink

Carbon system, ALLOW_CARBON active (5): R_OP, Kdoc, Kpremin_C, Kdissc, wpic_sink

★ = tuned by Carroll 2020 Green's functions (5 of 103 in init_fixed.F; the 6th R_PICPOC override lives in generate_phyto.F:484).

A.2 Derived equalities (6)

Kpremin_N (= Kpremin_P), Kpremin_Fe (= Kpremin_P), wn_sink (= wp_sink), wfe_sink (= wp_sink), wsi_sink (= wp_sink), wc_sink (= wp_sink).

A.3 Dead in this build (11)

ALLOW_DENIT undef: depthdenit, denit_np
ALLOW_DIAZ undef: diaz_growfac, val_R_NP_diaz, val_RFeP_diaz
ALLOW_MUTANTS undef: prochlPsat (commented "used only for mutants")
DAR_DIAG_DIVER undef: diver_thresh0, diver_thresh1, diver_thresh2, diver_thresh3, diver_thresh4

A.4 Unit conversions / physical constants (3)

parconv (W/m² → µEin), permil (1/1024.5, density conversion), Pa2Atm (Pa → atm).

Appendix B — Darwin 1 (`darwin_generate_phyto.F`) hardcoded per-phyto identity traits¶

7 distinct trait arrays × 5 phyto types = 35 individual values:

physize(np), phyto_esd(np), phyto_vol(np), diacoc(np), diazotroph(np), nsource(np), ap_type(np).

Plus one inline Green's-functions override at line 484: R_PICPOC(np) = 0.04245 for np = 2, 3, 8 (only np = 2, 3 valid since npmax = 5).

Appendix C — Darwin 3 (`v06/llc270` namelists) full parameter list¶

100 distinct tunable parameter names total.

C.1 &DARWIN_FORCING_PARAMS (20)

darwin_inscal_iron, darwin_inscal_ventHe3, darwin_inscal_DOCrunoff, darwin_inscal_DONrunoff, R_DOFe_DOP_runoff, darwin_inscal_DOPrunoff, R_NO3_DIN_runoff, R_NO2_DIN_runoff, R_NH4_DIN_runoff, darwin_inscal_DINrunoff, R_DFe_DIP_runoff, R_DIP_IP_runoff, darwin_inscal_IPrunoff, darwin_inscal_DSirunoff, darwin_inscal_POCrunoff, R_POFe_POP_runoff, darwin_inscal_POPrunoff, darwin_inscal_PONrunoff, R_ALK_DIC_runoff, darwin_inscal_DICrunoff.

C.2 &DARWIN_PARAMS (29)

tempCoeffArr, PARmin, alpfe, freefemax, depthfesed, scav_tau, ligand_tot, scav_POC_wgt, scav_PSi_wgt, scav_PIC_wgt, kdoc, kdop, kdon, kdofe, kPOC, kPOP, kPON, kPOFe, kPOSi, phygrazmin, hollexp, wC_sink, wN_sink, wP_sink, wFe_sink, wSi_sink, wPIC_sink, SURFDICMIN, SURFALKMIN.

C.3 &DARWIN_CDOM_PARAMS (5)

fracCDOM, cdomdegrd, CDOMbleach, PARCDOM, CDOMcoeff.

C.4 &DARWIN_RADTRANS_PARAMS (10)

Scalars (7): darwin_Sdom, darwin_aCDOM_fac, darwin_part_size_P, darwin_rCDOM, darwin_RPOC, darwin_absorpSlope, darwin_bbbSlope.

Spectral arrays of 13 values each (3): darwin_scatSwitchSizeLog, darwin_scatSlopeSmall, darwin_scatSlopeLarge.

C.5 &DARWIN_TRAIT_PARAMS (28)

a_R_PICPOC, a_Xmin, a_phytoTempAe, a_mQyield, a_chl2cmax, a_acclimtimescl, logvolbase, logvolinc, logvol0ind, a_biosink, b_biosink, a_PCmax, a_PCmax_denom, b_PCmax, a_Qpmin, a_Qpmax, grp_ExportFracPreyPred, a_R_ChlC, a_grazemax, b_grazemax, a_phytoTempExp2, a_R_PC, a_R_FeC, a_R_NC, a_R_SiC, a_kgrazesat, b_kgrazesat, grp_ass_eff.

C.6 &DARWIN_TRAITS from data.traits (8)

EXPORTFRACMORT, EXPORTFRACMORT2, PALAT, ASSEFF, GRAZEMAX, EXPORTFRACPREYPRED, MORT, MORT2.

C.7 Excluded from the 100 tunables (for the record)

File paths, dates, periods (51 in &DARWIN_FORCING_PARAMS): ironFile, ironPeriod, pCO2File, pCO2startdate1, pCO2startdate2, pCO2period, ventHe3File, ventHe3Period, the 12 runoff *file/*startdate1/*startdate2/*period quartets (48 names), darwin_useEXFwind, darwin_useQsw, darwin_useSEAICE (3 booleans).
Interpolation grid metadata (28 in &DARWIN_INTERP_PARAMS): 10 *_interpMethod flags, 18 lon0/lon_inc/lat0/lat_inc/nlon/nlat for ventHe3, iron, pCO2.
Numerical config in &DARWIN_PARAMS (8): darwin_chlIter0, darwin_pickupSuff, darwin_chlInitBalanced, diaz_ini_fac (dead, ALLOW_DIAZ undef), darwin_seed, darwin_disscSelect, plus 2 commented-out: selectPHsolver, selectK1K2const.
Commented-out CDOM stoichiometric ratios (3): R_NP_CDOM, R_FeP_CDOM, R_CP_CDOM.
RADTRANS file paths + boolean (4): darwin_waterabsorbFile, darwin_phytoabsorbFile, darwin_particleabsorbFile, darwin_allomSpectra.
TRAIT_PARAMS identity + classification (20): grp_names, grp_nplank, grp_photo, grp_pred, grp_prey, grp_hasSi, grp_hasPIC, grp_DIAZO, grp_useNH4, grp_useNO2, grp_useNO3, grp_combNO, grp_bacttype, grp_aerobic, grp_denit, grp_tempMort, grp_tempMort2, grp_aptype, darwin_effective_ksat, darwin_select_kn_allom.