\(\newcommand{\p}[1]{\frac{\partial }{\partial #1}}\) \(\newcommand{\pp}[2]{\frac{\partial #1}{\partial #2}}\) \(\newcommand{\dd}[2]{\frac{d #1}{d #2}}\) \(\newcommand{\h}{\frac{1}{2}}\) \(\newcommand{\op}[1]{\operatorname{#1}}\)
8.7.3.25. 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