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91d71e4089 Oliv* .. include:: ../defs.hrst
                 
                 Change Log
                 ^^^^^^^^^^
                 
                 (bug fixes and breaking changes in bold)
                 
fba8673244 Oliv* 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
                 
8916dab93b Oliv* - 2022-03-30 Add code for internal carbon store and exudation
81872c4188 Oliv* - 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
                 
383b27034c Oliv* - 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
91d71e4089 Oliv* - 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
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 123.


 - 2021-05-27 Add ecosystem tendency diagnostics without sink/swim: ‘gECO##’
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 124.


 - 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
                 

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