.. include:: ../defs.hrst Change Log ^^^^^^^^^^ (bug fixes and breaking changes in bold) darwin_ckpt69b - 2024-10-04 **Revert scavenging defaults to POP-based equivalents: only POC scavenges** - 2024-10-04 Add per-type diagnostics for limitation factors etc darwin_ckpt68z - 2024-06-25 Fix diagnostics call for sedFe - 2024-06-25 Add RADI sediment fluxes to cons check - 2024-06-25 **Rescale RADI sediment fluxes for NLFS** darwin_ckpt68x - 2024-04-05 **Really use surfSiMin** darwin_ckpy68v - 2024-01-18 Add oasim package - 2024-01-18 Add option to use diel solar zenith angle - 2024-01-17 **Fix case RT_useMeanCosSolz=.FALSE.** darwin_ckpt68p - 2023-04-19 Add cons check for implicit linear free surface - 2023-04-19 **Write Chlorophyll to pickup with radtrans** - 2023-04-19 **Mask POP-based sediment source with shelfice** - 2023-04-19 **Use mask at actual k for saphe coeffs** - 2023-03-16 **Fix unit conversion for Munhoven solver** - 2023-03-16 **Mask sinking properly with shelfice** darwin_ckpt68o - 2023-02-27 **Update use pload option, use surf_pRef** - 2023-02-26 Add RADI sediment model - 2023-02-25 Add Naviaux calcite dissolution rate - 2023-02-25 Add Keir calcite dissolution rate - 2023-02-25 Add carbonate and calcite saturation diags - 2023-02-25 Compute calcite saturation ratio OmegaC - 2023-02-21 Add Munhoven solver darwin_ckpt68n - 2023-01-03 **Add scavenging by POC, POSi and PIC** - 2023-01-03 Add iron source from hydrothermal vents - 2023-01-03 Add ventHe3 forcing darwin_ckpt68m - 2022-11-25 **Fix freeFeLs diagnostic** - 2022-10-31 **Avoid division by very small numbers** - 2022-10-31 Only write darwin cons info at beginning of longstep - 2022-10-28 **Fix mortality source for CDOM in carbon units** darwin_ckpt68l - 2022-10-19 Avoid division by zero with inhibGeider - 2022-10-17 **Add missing initialization for LS_fwFlux** - 2022-09-26 Add nutrient runoff to conservation check - 2022-09-23 Add nutrient runoff forcing darwin_ckpt68k - 2022-08-23 Fix O2 consumption diag and cons check - 2022-06-29 Add cons correction from precip, evap, runoff with non-linear free surface - 2022-06-29 Add cons correction due to bottom sinking - 2022-06-29 Rescale sinking fluxes for nonlinear free surface - 2022-06-29 Rescale surface and sediment fluxes for NLFS - 2022-06-29 Rescale alkalinity flux by hFacC - 2022-06-29 Overhaul conservation check - 2022-06-29 Add conservation check before thermodynamics - 2022-06-29 Only call second darwin_fe_chem if DARWIN_MINFE - 2022-06-29 Always include PIC code - 2022-06-29 Check that bacteria do not have silica - 2022-06-29 Maintain bacterial elemental ratios with quotas darwin_ckpt68i - 2022-03-30 Add code for internal carbon store and exudation - 2022-03-30 **Fix conservation of non-quota elems with parameterized respiration** - 2022-03-30 **Adjust uptake of non-quota elements for synthcost** - 2022-03-30 **Keep iron limit when using FEQUOTA without Geider** - 2022-03-23 Add per-type growth diagnostics HP####, HC####, GrGC#### darwin_ckpt68g - 2022-02-16 Darwin doc overhaul - 2022-02-12 Add option for CDOM to be in carbon units - 2022-02-12 Use applied pressure for pressure correction - 2022-02-12 Make sure dissociation constants are on the same pH scale - 2022-02-12 Add diagnostics: apCO2, apCO2sat, fCO2, freeFeLs, runoff tendencies, more consumption and source diagnostics - 2022-01-31 Make DARWIN_INDICES.h work better in code mods dir - 2022-01-30 **Fix bug with silica quotas but no Chl quotas** - 2022-01-14 merge checkpoint68f of MITgcm - 2022-01-13 **Fix benign bug in surfforcing diagnostics** - 2021-12-10 merge checkpoint68e of MITgcm darwin_ckpt68d - 2021-10-04 merge checkpoint68d of MITgcm - 2021-08-25 Add growth rate diagnostics 'PC####' - 2021-08-25 Add biomass and Chlorophyll diags, 'plankC' and 'Chl' darwin_ckpt68b - 2021-08-24 merge checkpoint68b of MITgcm darwin_ckpt68a - 2021-07-23 merge checkpoint68a of MITgcm - 2021-07-23 Fix "Add more carbon flux diagnostics" - 2021-05-28 Update diagnostics in docs merge checkpoint67z of MITgcm - 2021-05-27 Add ecosystem tendency diagnostics without sink/swim: ‘gECO##’ - 2021-05-27 Add more carbon flux diagnostics: ‘fluxO2’, ‘VfluxO2’, ‘VfluxAlk’ (see fix above) - 2021-05-27 **Take PIC into account for respiration and exudation** - 2021-05-27 Error if bacteria or predators have PIC - 2021-05-27 Add Coccolithophore shells to linfs conserve - 2021-05-28 Do not write nonconserving terms at beginning of time step - 2021-05-28 Add more sources of nonconservation to check - 2021-05-27 **Fix bug with DARWIN_ALLOW_DENIT and bacteria** - caused non-conservation - 2021-05-27 **Also turn off POSi remin and consum at low O2 and NO3** merge checkpoint67y of MITgcm - 2021-04-24 Error if radtrans compiled but not used with darwin - 2021-04-18 Allow to compile radtrans without sun package - 2021-04-23 Add radtrans_check and error if used without enable merge checkpoint67x of MITgcm - 2021-04-09 Add comment about flux diags units and sign to docs - 2021-01-29 Update darwin docs - 2021-01-29 Simplify units of plankton IOPs - 2021-01-25 Add LGR encoding for Greek unicode characters in docs - 2021-01-15 Add DARWIN_TEMP_VERSION 4 - 2021-01-22 Add separate temperature function for bacteria merge checkpoint67w of MITgcm merge checkpoint67v of MITgcm - 2021-01-29 Move aphy_chl_ave to params - 2021-02-04 **Fix loop range for DARWIN_SCATTER_CHL** - 2021-01-14 Add carbonspecific spectral plankton absorption - 2021-01-12 Fix units of fugfCO2 diagnostic - 2021-01-11 **Fix filling of fugfCO2 diagnostic** merge checkpoint67u of MITgcm merge checkpoint67t of MITgcm - 2020-10-28 Clean up and update darwin diags table in docs merge checkpoint67s of MITgcm merge checkpoint67r of MITgcm - 2020-06-07 Clean up some comments - 2020-06-07 Update docs - 2020-06-07 Remove nPPplank, nGRplank, nGrGn - 2020-03-19 Add diagnostics for pertype grazing gains merge checkpoint67q of MITgcm - 2020-03-12 Document new iron sediment source formulation - 2020-03-12 Make iron sediment source in terms of POC merge checkpoint67p of MITgcm merge checkpoint67o of MITgcm merge checkpoint67n of MITgcm - 2019-10-17 Avoid division by zero merge checkpoint67m of MITgcm - 2019-10-10 Eliminate more traces of gud - 2019-10-08 merge master of MITgcm - 2019-10-03 Add soluble iron input diagnostic - 2019-08-12 Rearrange EXF interpolation header files merge checkpoint67l of MITgcm - 2019-08-07 Add docs for darwin and radtrans packages - 2019-02-19 add \op macro as an abbreviation for \operatorname - 2019-08-06 Replace ksatPOM, ksatDOM by trait parameters a_ksatPON, a_ksatDON - 2019-07-31 Describe parameters in code - 2019-07-25 Fix units for oxygen diagnostic - 2019-07-31 **Move phymin to trait parameters** - 2019-08-06 Add \*RepCycle parameters to radtrans pkg merge checkpoint67k of MITgcm - 2019-07-23 Avoid division by zero for zero quota - 2019-07-18 **Replace bacteria uptake parameters by trait PCmax** - 2019-07-12 Document radtrans parameters in code - 2019-07-12 Add recalcitrant POC and CDOM parameters merge checkpoint67j of MITgcm - 2019-06-14 Fix names for palatability generation - 2019-05-13 Add DenitN diagnostic merge checkpoint67i of MITgcm - 2019-05-09 Add warning for use of default pCO2 value - 2019-05-08 Retire darwin_atmos_pCO2 - 2019-04-30 **Clip negative light values** - 2019-04-30 Indent cpp directives - 2019-04-26 Add \*RepCycle parameters - 2019-04-26 Set use of exf wind, seaice area and Qsw in namelist - 2019-04-26 Remove parameter useDarwinYearlyFields - 2019-04-16 **Do not reduce light under ice if DARWIN_useQsw** - 2019-04-18 Add darwin_pickupSuff, defaulting to pickupSuff - 2019-04-18 Add diagnostic for CO2 fugacity factor - 2019-04-29 Add DARWIN_BOTTOM_SINK option - 2019-04-29 Add legacy chl initialization for no-PARfile case - 2019-04-02 Clean up preprocessor directives and code blocks - 2019-04-16 **Cut negatives in freefe** - 2019-04-26 Disable temp dependence for zooplankton with random trait generation - 2019-04-26 Add tempGraz trait - 2019-04-16 Retire mort*TempFuncMin, use tempMort* directly - 2019-05-01 **Replace regularization by conditionals** - 2019-05-02 Do not log kMinFeSed, kMaxFeSed before they are computed - 2019-04-01 Remove unused parameters expPref, expPalat - 2019-04-08 Put nitrogen conservation numbers on one line - 2019-04-02 Shorten ptracers units (for netcdf output) - 2019-04-02 Fix for python 3.X merge checkpoint67h of MITgcm - 2019-02-21 Move chl init parameters to DARWIN_PARAMS - 2018-02-26 add darwin package - 2018-02-26 update darwin call interface - 2018-09-19 add radtrans package - 2018-02-19 add sun package MITgcm checkpoint67g