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Merge pull request #12 from PALEOtoolkit/split_ocean
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Split up ReactionOceanCOPSE
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@sjdaines
sjdaines authored Jul 9, 2022
2 parents 7bb2413 + 12dd12a commit 0b58a3c
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Showing 9 changed files with 377 additions and 185 deletions.
4 changes: 2 additions & 2 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "PALEOcopse"
uuid = "4a6ed817-0e58-48c6-8452-9e9afc8cb508"
authors = ["sd336 "]
version = "0.3.1"
version = "0.4.0"

[deps]
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Expand All @@ -19,7 +19,7 @@ Documenter = "0.27"
Infiltrator = "1.0"
Interpolations = "0.13"
MAT = "0.10"
PALEOboxes = "0.19.1"
PALEOboxes = "0.19.1, 0.20.0"
PALEOmodel = "0.15.1"
Plots = "1.0"
Roots = "1.0, 2.0"
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5 changes: 3 additions & 2 deletions docs/src/PALEOcopse.md
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Expand Up @@ -68,16 +68,17 @@ CurrentModule = PALEOcopse.Ocean
```

```@docs
OceanCOPSE.ReactionOceanCOPSE
OceanCOPSE.ReactionMarineBiotaCOPSE
OceanCOPSE.ReactionOceanBurialCOPSE
```

## Ocean floor
```@meta
CurrentModule = PALEOcopse.Oceanfloor
```

### Seafloor weathering
```@docs
CarbBurial.ReactionCarbBurialAlk
Weathering.ReactionSeafloorWeathering
```

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16 changes: 12 additions & 4 deletions examples/COPSE/COPSE_reloaded_bergman2004_cfg.yaml
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Expand Up @@ -445,8 +445,11 @@ model1:
R:initial_value: 4e19
R:initial_delta: 20.0 # per mil

ocean_copse:
class: ReactionOceanCOPSE
marinebiota_copse:
class: ReactionMarineBiotaCOPSE

oceanburial_copse:
class: ReactionOceanBurialCOPSE
parameters:
# Marine organic carbon burial
f_mocb : 'original' # COPSE Bergman (2004) functional form
Expand Down Expand Up @@ -478,10 +481,15 @@ model1:
DIC_delta: DIC_delta # provided by CIsotopes
# DIC*: atmocean.A # dont do this !!! (overwrites DIC_delta with atmocean.A_delta)
# Route O -> atmocean.O
O*: atmocean.O*
O: atmocean.O # O, O_*, but NOT OX*
O_*: atmocean.O_*

oceanfloor:

reactions:
carbburial:
class: ReactionCarbBurialAlk
variable_links:
DIC_sms: atmocean.A_sms


oceansurface:
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32 changes: 21 additions & 11 deletions examples/COPSE/COPSE_reloaded_reloaded_cfg.yaml
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Expand Up @@ -568,19 +568,11 @@ model1:
R:initial_value: 1.2e17
R:initial_delta: 0.708 # reasonable average value for Phanerozoic

ocean_copse:
class: ReactionOceanCOPSE
variable_links:
DIC_sms: atmocean.A_sms
DIC_delta: DIC_delta # provided by CIsotopes
# DIC*: atmocean.A # dont do this !!! (overwrites DIC_delta with atmocean.A_delta)
O*: atmocean.O*
CAL_norm: global.CAL_NORM # [Ca] from forcing
marinebiota_copse:
class: ReactionMarineBiotaCOPSE
parameters:
newp0: 225.956
CNsea0: 37.5
CPsea0: 250.0


f_anoxia: newanoxia
k_logistic: 12.0
k_uptake: 0.5
Expand All @@ -591,6 +583,19 @@ model1:
k3_nfix: 8.667e12
k4_denit: 4.3e12

oceanburial_copse:
class: ReactionOceanBurialCOPSE
variable_links:
DIC_sms: atmocean.A_sms
DIC_delta: DIC_delta # provided by CIsotopes
# DIC*: atmocean.A # dont do this !!! (overwrites DIC_delta with atmocean.A_delta)
O: atmocean.O # relink O, O_*, NOT OX*
O_*: atmocean.O_*
CAL_norm: global.CAL_NORM # [Ca] from forcing
parameters:
CNsea0: 37.5
CPsea0: 250.0

f_mocb: original
f_mocb_b: 2.0
k2_mocb: 2.5e12
Expand All @@ -616,6 +621,11 @@ model1:


reactions:
carbburial:
class: ReactionCarbBurialAlk
variable_links:
DIC_sms: atmocean.A_sms

sfw:
class: ReactionSeafloorWeathering
parameters:
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9 changes: 5 additions & 4 deletions examples/COPSE/copse_reloaded_bergman2004_expts.jl
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Expand Up @@ -50,15 +50,16 @@ function copse_reloaded_bergman2004_expts(

elseif expt == "VCI"
# Fig.12 magenta
PB.setvalue!(PB.get_reaction(model, "ocean", "ocean_copse").pars.f_CPsea, "VCI")
PB.setvalue!(PB.get_reaction(model, "ocean", "oceanburial_copse").pars.f_CPsea, "VCI")

elseif expt == "mocbProdLinear"
# not shown in paper - mocb linearly proportional to new production
PB.setvalue!(PB.get_reaction(model, "ocean", "ocean_copse").pars.f_mocb_b, 1.0)
PB.setvalue!(PB.get_reaction(model, "ocean", "oceanburial_copse").pars.f_mocb_b, 1.0)

elseif expt == "noNcycle"
# not shown in paper
PB.setvalue!(PB.get_reaction(model, "ocean", "ocean_copse").pars.f_ncycle, false)
PB.setvalue!(PB.get_reaction(model, "ocean", "marinebiota_copse").pars.f_ncycle, false)
PB.setvalue!(PB.get_reaction(model, "ocean", "oceanburial_copse").pars.f_ncycle, false)

elseif length(expt) == 5 && expt[1] == "setpar"
# generic parameter set (setpar, <domain>, <reaction>, <parname>, <parvalue)
Expand Down Expand Up @@ -90,7 +91,7 @@ function copse_reloaded_bergman2004_expts(
end

# set parameters for steady-state
rct_ocean = PB.get_reaction(model, "ocean", "ocean_copse")
rct_ocean = PB.get_reaction(model, "ocean", "oceanburial_copse")
mtotpb = rct_ocean.pars.k2_mocb.v/rct_ocean.pars.CPsea0.v +rct_ocean.pars.k7_capb.v +rct_ocean.pars.k6_fepb.v
rct_degass = PB.get_reaction(model, "sedcrust", "sedcrust_copse")

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9 changes: 5 additions & 4 deletions examples/COPSE/copse_reloaded_reloaded_expts.jl
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Expand Up @@ -55,15 +55,16 @@ function copse_reloaded_reloaded_expts(

elseif expt == "VCI"
# Fig.12 magenta
PB.set_parameter_value!(model, "ocean", "ocean_copse", "f_CPsea", "VCI")
PB.set_parameter_value!(model, "ocean", "oceanburial_copse", "f_CPsea", "VCI")

elseif expt == "mocbProdLinear"
# not shown in paper - mocb linearly proportional to new production
PB.set_parameter_value!(model, "ocean", "ocean_copse", "f_mocb_b", 1.0)
PB.set_parameter_value!(model, "ocean", "oceanburial_copse", "f_mocb_b", 1.0)

elseif expt == "noNcycle"
# not shown in paper
PB.set_parameter_value!(model, "ocean", "ocean_copse", "f_ncycle", false)
PB.set_parameter_value!(model, "ocean", "marinebiota_copse", "f_ncycle", false)
PB.set_parameter_value!(model, "ocean", "oceanburial_copse", "f_ncycle", false)

elseif length(expt) == 5 && expt[1] == "setpar"
# generic parameter set (setpar, <domain>, <reaction>, <parname>, <parvalue)
Expand Down Expand Up @@ -92,7 +93,7 @@ function copse_reloaded_reloaded_expts(
end

# set parameters for carbonate-silicate weathering steady-state
rct_ocean = PB.get_reaction(model, "ocean", "ocean_copse")
rct_ocean = PB.get_reaction(model, "ocean", "oceanburial_copse")
mtotpb = rct_ocean.pars.k2_mocb.v/rct_ocean.pars.CPsea0.v +rct_ocean.pars.k7_capb.v +rct_ocean.pars.k6_fepb.v
rct_degass = PB.get_reaction(model, "sedcrust", "sedcrust_copse")
rct_sfw = PB.get_reaction(model, "oceanfloor", "sfw")
Expand Down
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Registration pull request created: JuliaRegistries/General/63912

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.4.0 -m "<description of version>" 0b58a3c9658e29b49a935a7ad2e11680a5df89cc
git push origin v0.4.0

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