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uwagurauwagura
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Merge pull request #247 from NOAA-GFDL/fix/automodule_segfault
Turn submodule update back on after segfault issue was resolved
2 parents 30f2b00 + 5bb27c1 commit b304307

11 files changed

Lines changed: 359 additions & 125 deletions

.github/workflows/update-submodules._yml renamed to .github/workflows/update-submodules.yml

File renamed without changes.

‎exps/NEP10.COBALT/COBALT_parameter_doc.all‎

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@@ -342,6 +342,10 @@ mort_Lg = 0.0 ! [day-1] default = 0.0
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! mortality (cell death) rate constant for large phytoplankton @ 0 deg. C
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mort_Md = 0.0 ! [day-1] default = 0.0
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! mortality (cell death) rate constant for medium phytoplankton @ 0 deg. C
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phi_sidiss_mort_Md = 0.0 ! [none] default = 0.0
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! fraction of medium diatom silica dissolved during respiration and mortality
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phi_sidiss_mort_Lg = 0.0 ! [none] default = 0.0
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! fraction of larger diatom silica dissolved during respiration and mortality
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exu_Sm = 0.13 ! [none] default = 0.13
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! fraction of small phytoplankton net primary production exuded as dissolved
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! organic material
@@ -519,6 +523,12 @@ phi_sldop_mdz = 0.045 ! [none] default = 0.045
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phi_sldop_lgz = 0.0 ! [none] default = 0.0
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! fraction of P ingestion by large zooplankton to semi-labile dissolved organic
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! phosphorus
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phi_det_si_smz = 0.0 ! [none] default = 0.0
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! fraction of silica ingestion by small zooplankton to si detritus
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phi_det_si_mdz = 0.15 ! [none] default = 0.15
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! fraction of silica ingestion by medium zooplankton to si detritus
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phi_det_si_lgz = 0.3 ! [none] default = 0.3
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! fraction of silica ingestion by large zooplankton to si detritus
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phi_ldon_vir = 0.625 ! [none] default = 0.625
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! fraction of viral lysis of N to labile dissolved organic nitrogen
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phi_srdon_vir = 0.075 ! [none] default = 0.075
@@ -600,8 +610,6 @@ remin_ramp_scale = 50.0 ! [m] default = 50.0
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! depth scale from the surface over which remineralization ramps up
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gamma_ndet = 3.306878306878307E-06 ! [s-1] default = 3.306878306878307E-06
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! Remineralization rate for unprotected organic matter
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gamma_ndet_fast = 3.306878306878307E-06 ! [s-1] default = 3.306878306878307E-06
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! Remineralization rate for fast-sinking unprotected organic matter
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rpcaco3 = 0.0880503144654088 ! [mol N mol Ca-1] default = 0.0880503144654088
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! Organic matter protection from CaCO3
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rplith = 8.176100628930818E-04 ! [mol N g lith-1] default = 8.176100628930818E-04

‎exps/NEP10.COBALT/MOM_parameter_doc.all‎

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‎exps/NEP10.COBALT/MOM_parameter_doc.debugging‎

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@@ -48,6 +48,10 @@ DEBUG_REDUNDANT = False ! [Boolean] default = False
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OBC_DEBUGGING_TESTS = False ! [Boolean] default = False
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! If true, do additional calls resetting certain values to help verify the
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! correctness of the open boundary condition code.
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OBC_REVERSE_SEGMENT_ORDER = False ! [Boolean] default = False
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! If true, store the OBC segments internally and handle them in the reverse
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! order from that with which they are specified via external parameters to test
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! for dependencies on the order with which the OBC segments are applied.
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! === module MOM_verticalGrid ===
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! Parameters providing information about the vertical grid.

‎exps/NEP10.COBALT/MOM_parameter_doc.short‎

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‎exps/NEP10.COBALT/SIS_parameter_doc.all‎

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@@ -283,6 +283,11 @@ NUDGE_SEA_ICE = False ! [Boolean] default = False
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TRANSMUTE_SEA_ICE = False ! [Boolean] default = False
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! If true, allow ice to be transmuted directly into seawater with a spatially
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! varying rate as a form of outflow open boundary condition.
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DO_BRINE_PLUME = False ! [Boolean] default = False
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! If true, split heat and salt fluxes to the ocean into brine plumes and other.
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SIS_SPONGE = False ! [Boolean] default = False
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! If true, SIS sponges may be applied anywhere in the domain. The exact location
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! and properties of those sponges are specified via SIS_SPONGE_CONFIG.
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! === module SIS2_ice_thm (updates) ===
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! This sub-module does updates of the sea-ice due to thermodynamic changes.
@@ -398,6 +403,11 @@ LEMIEUX_LANDFAST = False ! [Boolean] default = False
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! If true, turn on Lemieux landfast ice parameterization.
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ITD_LANDFAST = False ! [Boolean] default = False
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! If true, turn on probabilistic landfast ice parameterization.
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NEGLECT_MASSLESS_ICE_SNOW_POND = False ! [Boolean] default = False
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! If True, category ice, snow or pond mass per ocean cell area less than
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! CONTINUITY_H_NEGLECT are not transported out of a cell. The default value is
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! set to retain previous answers, but new experiments should set to True with a
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! suitably small value of CONTINUITY_H_NEGLECT.
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RECATEGORIZE_ICE = True ! [Boolean] default = True
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! If true, readjust the distribution into ice thickness categories after
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! advection.

‎exps/NWA12.COBALT/COBALT_parameter_doc.all‎

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -342,6 +342,10 @@ mort_Lg = 0.0 ! [day-1] default = 0.0
342342
! mortality (cell death) rate constant for large phytoplankton @ 0 deg. C
343343
mort_Md = 0.0 ! [day-1] default = 0.0
344344
! mortality (cell death) rate constant for medium phytoplankton @ 0 deg. C
345+
phi_sidiss_mort_Md = 0.0 ! [none] default = 0.0
346+
! fraction of medium diatom silica dissolved during respiration and mortality
347+
phi_sidiss_mort_Lg = 0.0 ! [none] default = 0.0
348+
! fraction of larger diatom silica dissolved during respiration and mortality
345349
exu_Sm = 0.13 ! [none] default = 0.13
346350
! fraction of small phytoplankton net primary production exuded as dissolved
347351
! organic material
@@ -519,6 +523,12 @@ phi_sldop_mdz = 0.045 ! [none] default = 0.045
519523
phi_sldop_lgz = 0.0 ! [none] default = 0.0
520524
! fraction of P ingestion by large zooplankton to semi-labile dissolved organic
521525
! phosphorus
526+
phi_det_si_smz = 0.0 ! [none] default = 0.0
527+
! fraction of silica ingestion by small zooplankton to si detritus
528+
phi_det_si_mdz = 0.15 ! [none] default = 0.15
529+
! fraction of silica ingestion by medium zooplankton to si detritus
530+
phi_det_si_lgz = 0.3 ! [none] default = 0.3
531+
! fraction of silica ingestion by large zooplankton to si detritus
522532
phi_ldon_vir = 0.625 ! [none] default = 0.625
523533
! fraction of viral lysis of N to labile dissolved organic nitrogen
524534
phi_srdon_vir = 0.075 ! [none] default = 0.075
@@ -600,8 +610,6 @@ remin_ramp_scale = 50.0 ! [m] default = 50.0
600610
! depth scale from the surface over which remineralization ramps up
601611
gamma_ndet = 3.306878306878307E-06 ! [s-1] default = 3.306878306878307E-06
602612
! Remineralization rate for unprotected organic matter
603-
gamma_ndet_fast = 3.306878306878307E-06 ! [s-1] default = 3.306878306878307E-06
604-
! Remineralization rate for fast-sinking unprotected organic matter
605613
rpcaco3 = 0.0880503144654088 ! [mol N mol Ca-1] default = 0.0880503144654088
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! Organic matter protection from CaCO3
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rplith = 8.176100628930818E-04 ! [mol N g lith-1] default = 8.176100628930818E-04

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