PALEOcopse Reactions

ReactionForce_CK_Solar

SOLAR forcing (incident solar flux at Earth, W m^-2)

Parameters

Methods and Variables

• do_force_CK_solar
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • SOLAR (W m-2), VT_ReactProperty, description="incident solar flux at Earth"

ReactionForce_UDWEbergman2004

COPSE Bergman(2004) forcings from file.

Provides:

• UPLIFT tectonic uplift. GEOCARB II (Berner 1994) based on Sr isotopes.
• DEGASS metamorphic and volcanic degassing. Bergman etal (2004), same as GEOCARB II (Berner 1994): Engerbretson etal (1992) seafloor subduction (spreading) rate 0 - 150Ma, Gaffin (1987) Paleo-sealevel based 570 - 150Ma
• EVO land plant evolution and colonisation. Bergman etal (2004)
• W biological enhancement of weathering. Bergman etal (2004)

Interpolates and optionally applies naive extrapolation of forcings into (constant) Precambrian and future

Methods and Variables

• do_force_UDWEbergman2004
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • UPLIFT (), VT_ReactProperty, description="tectonic uplift normalized to present. GEOCARB II (Berner 1994) based on Sr isotopes."
  • DEGASS (), VT_ReactProperty, description="metamorphic and volcanic degassing normalized to present"
  • EVO (), VT_ReactProperty, description="land plant evolution and colonisation"
  • W (), VT_ReactProperty, description="biological enhancement of weathering"

ReactionForce_Bbergman2004

Bforcing forcing, calcerous plankton evolution (COPSE 2004)

Methods and Variables

• do_force_Bbergman2004
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • Bforcing (), VT_ReactProperty, description="calcerous plankton evolution"

ReactionForce_CPlandrelbergman2004

CPland_relative forcing. CP land burial ratio doubles in permo-carboniferous (COPSE)

Methods and Variables

• do_force_CPlandrelbergman2004
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • CPland_relative (), VT_ReactProperty, description="normalized land CP burial ratio"

ReactionForce_spreadsheet

Generic forcing interpolated from values in spreadsheet.

Spreadsheet should contain a table of numeric data in sheet sheetname, with a single header row, and time in timecolumn and data in datacolumn.

Time from timecolumn is multiplied by timemultiplier to convert to PALEO model time.

Linearly interpolates in time tforce to set Variable forcename, and extrapolates into past and future, either to values in extrap_value_past, extrap_value_future, or to the closest spreadsheet value if these Parameters are NaN.

Implementation

Spreadsheet data is read using the Julia XLSX and DataFrames packages with

xf = XLSX.readxlsx(forcingfile)
df = XLSX.eachtablerow(xf[sheetname]) |> DataFrames.DataFrame

Parameters

• forcename[String]="FORCE", default_value="FORCE", description="name of forcing (this will be a variable name in global Domain)"
• datafolder[String]="/home/runner/work/PALEOcopse.jl/PALEOcopse.jl/src/Forcings", default_value="/home/runner/work/PALEOcopse.jl/PALEOcopse.jl/src/Forcings", description="folder for spreadsheet with forcing data"
• datafile[String]="", default_value="", description="spreadsheet with forcing data (path relative to 'datafolder')"
• sheetname[String]="Sheet1", default_value="Sheet1", description="sheet name in spreadsheet"
• timecolumn[Int64]=1, default_value=1, description="column with time data"
• timemultiplier[Float64]=-1.0e6, default_value=-1.0e6, description="factor to multiply 'timecolumn' by to convert to yr after present day (so times in past are -ve)"
• datacolumn[Int64]=2, default_value=2, description="column with forcing data"
• extrap_value_past[Float64]=1.0, default_value=1.0, description="extrapolate value for tforce before earliest value in spreadsheet (NaN to use earliest value)"
• extrap_value_future[Float64]=1.0, default_value=1.0, description="extrapolate value for tforce after latest value in spreadsheet (NaN to use latest value"

Methods and Variables for default Parameters

• do_force_spreadsheet
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • FORCE (), VT_ReactProperty, description="forcing interpolated from spreadsheet"

ReactionForce_LIPs

LIP basalt area and optional CO2 forcing ((Mills et al., 2014)), updated in (Lenton et al., 2018) COPSE Reloaded).

Reads spreadsheet table of LIP data, and creates per-LIP area vs time profile including weathering reduction in area. A default area reduction rate (applied to those LIPs where it is poorly constrained) is tuned to match overall modern continental flood basalt area.

If Parameter co2releasefield != NoCO2, a CO2 pulse (duration 2e5yr, magnitude from spreadsheet, -5 per mil) is output as LIP_CO2 and added to Variable flux_C -> fluxSedCrusttoAOcean.flux_C.

Parameters

• datafolder[String]="/home/runner/work/PALEOcopse.jl/PALEOcopse.jl/src/Forcings", default_value="/home/runner/work/PALEOcopse.jl/PALEOcopse.jl/src/Forcings", description="folder for forcing data 'datafile'"
• datafile[String]="CR_force_LIP_table.xlsx", default_value="CR_force_LIP_table.xlsx", description="spreadsheet with forcing data (path relative to 'datafolder')"
• present_day_CFB_area[Float64]=4.8e6 (km^2), default_value=4.8e6, description="present day continental flood basalt area"
• smoothempl[Bool]=false, default_value=false, description="smooth LIP basalt emplacement"
• co2releasefield[String]="NoCO2", default_value="NoCO2", allowed_values=["NoCO2", "CO2min", "CO2max"], description="LIP CO2 release"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_force_LIPs
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • CFB_area (km^2), VT_ReactProperty, description="LIP continental flood basalt area"
  • LIP_CO2 (mol yr-1), VT_ReactProperty, description="LIP CO2 release"
  • flux_C –> fluxSedCrusttoAOcean.flux_C (mol yr-1), VT_ReactContributor, description="LIP CO2 release"

ReactionModelBergman2004

Monolithic COPSE Bergman(2004) model, providing all biogeochemistry as a single Reaction in a single global Domain.

Requires reservoirs, forcings, and global temperature (ReactionGlobalTemperatureCK1992) to form a complete model.

Parameters

• k1_oxfrac[Float64]=0.86, default_value=0.86, description="initial oxic fraction"
• k2_mocb[Float64]=4.5e12 (mol/yr), default_value=4.5e12, description="ocean organic carbon burial"
• k3_nfix[Float64]=8.75e12 (mol/yr), default_value=8.75e12, description="nitrogen fixation"
• k4_denit[Float64]=4.3e12 (mol/yr), default_value=4.3e12, description="denitrification"
• k5_locb[Float64]=4.5e12 (mol/yr), default_value=4.5e12, description="land organic carbon burial"
• k6_fepb[Float64]=6.0e9 (mol/yr), default_value=6.0e9, description="Fe-P burial"
• k7_capb[Float64]=1.5e10 (mol/yr), default_value=1.5e10, description="Ca-P burial"
• k11_landfrac[Float64]=0.10345, default_value=0.10345, description="fract of weath P buried on land"
• k12_ccdeg[Float64]=6.65e12 (mol/yr), default_value=6.65e12, description="carbonate C degassing"
• k13_ocdeg[Float64]=1.25e12 (mol/yr), default_value=1.25e12, description="org C degassing"
• k14_carbw[Float64]=1.335e13 (mol/yr), default_value=1.335e13, description="carbonate weathering"
• k15_plantenhance[Float64]=0.15, default_value=0.15, description="weathering enhancement factor prior to vascular plant colonisation"
• k_fire[Float64]=100.0, default_value=100.0, description="fire feedback"
• k16_PANtoO[Float64]=3.762, default_value=3.762, description="For calculating mixing ratio O2 from normalised O2"
• k_silw[Float64]=NaN (mol/yr), default_value=NaN, description="silicate weathering"
• k10_phosw[Float64]=NaN (mol/yr), default_value=NaN, description="phosphorus weathering"
• k17_oxidw[Float64]=NaN (mol/yr), default_value=NaN, description="oxidative org carbon weathering"
• k21_pyrw[Float64]=5.3e11 (mol S/yr), default_value=5.3e11, description="pyrite weathering"
• k22_gypw[Float64]=1.0e12 (mol S/yr), default_value=1.0e12, description="gypsum weathering"
• k_pyrdeg[Float64]=0.0 (mol S/yr), default_value=0.0, description="pyrite degassing"
• k_gypdeg[Float64]=0.0 (mol S/yr), default_value=0.0, description="gypsum degassing"
• k_mpsb[Float64]=5.3e11 (mol S/yr), default_value=5.3e11, description="pyrite burial"
• k_mgsb[Float64]=1.0e12 (mol S/yr), default_value=1.0e12, description="gypsum burial"
• f_ocdeg[String]="O2indep", default_value="O2indep", allowed_values=["O2indep", "O2copsecrashprevent"], description="roll of orgC degassing at low pO2"
• f_temp[String]="CK1992", default_value="CK1992", description="functional form of temperature estimate"
• f_carbwC[String]="Cindep", default_value="Cindep", allowed_values=["Cindep", "Cprop"], description="C (carbonate reservoir) dependence of carbonate weathering"
• f_oxwO[String]="PowerO2", default_value="PowerO2", allowed_values=["PowerO2", "SatO2"], description="oxidative weathering functional form"
• f_oxw_a[Float64]=0.5, default_value=0.5, description="oxidative weathering dependency on O2 concentration"
• f_nfix_power[Float64]=2.0, default_value=2.0, description="SD update to BM Matlab code which has f_nfix_power : 1. This fixes discrepancy between P (phosphorus) and COPSE 5_14 (most visible in Cambrian)"
• f_nfix_nreplete[String]="Off", default_value="Off", allowed_values=["Off", "Sign"], description="Bug compatitibility with COPSE 5_14 C code, which has Sign)"
• newp0[Float64]=225.956, default_value=225.956, description=""
• f_CPsea[String]="Fixed", default_value="Fixed", allowed_values=["Fixed", "VCI"], description="Functional form of CPsea ratio"
• CPsea0[Float64]=250.0, default_value=250.0, description="for f_CPsea:"Fixed""
• f_CPsea_VCI_oxic[Float64]=217.0, default_value=217.0, description="Van Cappellen & Ingall (f_CPsea:"VCI") marine C/P burial ratio consts"
• f_CPsea_VCI_anoxic[Float64]=4340.0, default_value=4340.0, description="Van Cappellen & Ingall (f_CPsea:"VCI") marine C/P burial ratio consts"
• CNsea0[Float64]=37.5, default_value=37.5, description="Always fixed"
• f_mocb_b[Float64]=2.0, default_value=2.0, description="marine organic carbon burial power-law dependency on new production"
• f_pyrburial[String]="copse_O2", default_value="copse_O2", allowed_values=["copseO2", "copsenoO2"], description="Marine pyrite sulphur burial dependency on oxygen"
• f_cisotopefrac[String]="copse_base", default_value="copse_base", allowed_values=["fixed", "copsebase", "copsenoO2"], description="fractionation calculation method"
• f_sisotopefrac[String]="fixed", default_value="fixed", allowed_values=["fixed", "copse_O2"], description="S isotope fractionation calculation."

Methods and Variables

• do_stateandeqb
  • P (mol), VT_ReactDependency, description="Marine phosphorus"
  • N (mol), VT_ReactDependency, description="Marine nitrogen"
  • O (mol), VT_ReactDependency, description="Atm-ocean oxygen"
  • C (mol), VT_ReactDependency, description="Sedimentary carbonate"
  • G (mol), VT_ReactDependency, description="Sedimentary organic carbon"
  • A (mol), VT_ReactDependency, description="Atm-ocean inorganic carbon"
  • CAL (mol), VT_ReactDependency, description="Marine calcium"
  • GYP (mol), VT_ReactDependency, description="Sedimentary gypsum"
  • PYR (mol), VT_ReactDependency, description="Sedimentary pyrite"
  • S (mol), VT_ReactDependency, description="Marine sulphate"
  • P_norm (), VT_ReactDependency, description="normalized Marine phosphorus"
  • N_norm (), VT_ReactDependency, description="normalized Marine nitrogen"
  • O_norm (), VT_ReactDependency, description="normalized Atm-ocean oxygen"
  • C_norm (), VT_ReactDependency, description="normalized Sedimentary carbonate"
  • C_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary carbonate"
  • G_norm (), VT_ReactDependency, description="normalized Sedimentary organic carbon"
  • G_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary organic carbon"
  • A_norm (), VT_ReactDependency, description="normalized Atm-ocean inorganic carbon"
  • A_delta (per mil), VT_ReactDependency, description="isotope delta Atm-ocean inorganic carbon"
  • CAL_norm (), VT_ReactDependency, description="normalized Marine calcium"
  • GYP_norm (), VT_ReactDependency, description="normalized Sedimentary gypsum"
  • GYP_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary gypsum"
  • PYR_norm (), VT_ReactDependency, description="normalized Sedimentary pyrite"
  • PYR_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary pyrite"
  • S_norm (), VT_ReactDependency, description="normalized Marine sulphate"
  • S_delta (per mil), VT_ReactDependency, description="isotope delta Marine sulphate"
  • tforce (yr), VT_ReactDependency, description="time for external forcings"
  • SOLAR (W m-2), VT_ReactDependency, description="solar luminosity"
  • UPLIFT (), VT_ReactDependency, description="uplift scaling"
  • DEGASS (), VT_ReactDependency, description="degassing scaling"
  • W (), VT_ReactDependency, description="plant weathering scaling"
  • EVO (), VT_ReactDependency, description="plant evolution scaling"
  • Bforcing (), VT_ReactDependency, description="calcerous plankton evolution"
  • CPland_relative (), VT_ReactDependency, description="land CP burial ratio scaling"
  • TEMP (K), VT_ReactDependency, description="global temperature"
  • pO2PAL (), VT_ReactProperty, description="atmospheric oxygen relative to present-day"
  • pCO2PAL (), VT_ReactProperty, description="atmospheric pCO2 relative to present-day"
  • pCO2atm (atm), VT_ReactProperty, description="atmospheric pCO2"
  • d_mccb (per mil), VT_ReactProperty, description="D13C fractionation carbonate - atm-ocean inorganic carbon"
  • d_locb (per mil), VT_ReactProperty, description="D13C fractionation land organic carbon burial - atm-ocean inorganic carbon"
  • d_mocb (per mil), VT_ReactProperty, description="D13C fractionation marine organic carbon burial - atm-ocean inorganic carbon"
  • mccb_delta (per mil), VT_ReactProperty, description="D13C fractionation of marine calcium carbonate burial"
  • D_mpsb (per mil), VT_ReactProperty, description="D34S fractionation pyrite - marine sulphate"
• do_react
  • P (mol), VT_ReactDependency, description="Marine phosphorus"
  • N (mol), VT_ReactDependency, description="Marine nitrogen"
  • O (mol), VT_ReactDependency, description="Atm-ocean oxygen"
  • C (mol), VT_ReactDependency, description="Sedimentary carbonate"
  • G (mol), VT_ReactDependency, description="Sedimentary organic carbon"
  • A (mol), VT_ReactDependency, description="Atm-ocean inorganic carbon"
  • CAL (mol), VT_ReactDependency, description="Marine calcium"
  • GYP (mol), VT_ReactDependency, description="Sedimentary gypsum"
  • PYR (mol), VT_ReactDependency, description="Sedimentary pyrite"
  • S (mol), VT_ReactDependency, description="Marine sulphate"
  • P_norm (), VT_ReactDependency, description="normalized Marine phosphorus"
  • N_norm (), VT_ReactDependency, description="normalized Marine nitrogen"
  • O_norm (), VT_ReactDependency, description="normalized Atm-ocean oxygen"
  • C_norm (), VT_ReactDependency, description="normalized Sedimentary carbonate"
  • C_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary carbonate"
  • G_norm (), VT_ReactDependency, description="normalized Sedimentary organic carbon"
  • G_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary organic carbon"
  • A_norm (), VT_ReactDependency, description="normalized Atm-ocean inorganic carbon"
  • A_delta (per mil), VT_ReactDependency, description="isotope delta Atm-ocean inorganic carbon"
  • CAL_norm (), VT_ReactDependency, description="normalized Marine calcium"
  • GYP_norm (), VT_ReactDependency, description="normalized Sedimentary gypsum"
  • GYP_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary gypsum"
  • PYR_norm (), VT_ReactDependency, description="normalized Sedimentary pyrite"
  • PYR_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary pyrite"
  • S_norm (), VT_ReactDependency, description="normalized Marine sulphate"
  • S_delta (per mil), VT_ReactDependency, description="isotope delta Marine sulphate"
  • tforce (yr), VT_ReactDependency, description="time for external forcings"
  • SOLAR (W m-2), VT_ReactDependency, description="solar luminosity"
  • UPLIFT (), VT_ReactDependency, description="uplift scaling"
  • DEGASS (), VT_ReactDependency, description="degassing scaling"
  • W (), VT_ReactDependency, description="plant weathering scaling"
  • EVO (), VT_ReactDependency, description="plant evolution scaling"
  • Bforcing (), VT_ReactDependency, description="calcerous plankton evolution"
  • CPland_relative (), VT_ReactDependency, description="land CP burial ratio scaling"
  • TEMP (K), VT_ReactDependency, description="global temperature"
  • pO2PAL (), VT_ReactDependency, description="atmospheric oxygen relative to present-day"
  • pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 relative to present-day"
  • pCO2atm (atm), VT_ReactDependency, description="atmospheric pCO2"
  • d_mccb (per mil), VT_ReactDependency, description="D13C fractionation carbonate - atm-ocean inorganic carbon"
  • d_locb (per mil), VT_ReactDependency, description="D13C fractionation land organic carbon burial - atm-ocean inorganic carbon"
  • d_mocb (per mil), VT_ReactDependency, description="D13C fractionation marine organic carbon burial - atm-ocean inorganic carbon"
  • mccb_delta (per mil), VT_ReactDependency, description="D13C fractionation of marine calcium carbonate burial"
  • D_mpsb (per mil), VT_ReactDependency, description="D34S fractionation pyrite - marine sulphate"
  • V_T (), VT_ReactProperty, description="effect of temp on VEG"
  • V_co2 (), VT_ReactProperty, description="effect of CO2 on VEG"
  • V_o2 (), VT_ReactProperty, description="effect of O2 on VEG"
  • V_npp (), VT_ReactProperty, description="full VEG limitation"
  • mrO2 (), VT_ReactProperty, description="atmospheric O2 mixing ratio"
  • ignit (), VT_ReactProperty, description="ignition probability"
  • firef (), VT_ReactProperty, description="effect of fire on VEG"
  • VEG (), VT_ReactProperty, description="Mass of terrestrial biosphere"
  • f_preplant (), VT_ReactProperty, description="Pre-plant silicate weathering T and pCO2 factor"
  • f_plant (), VT_ReactProperty, description="Plant silicate weathering T and pCO2 factor"
  • g_preplant (), VT_ReactProperty, description="Pre-plant carbonate weathering T and pCO2 factor"
  • g_plant (), VT_ReactProperty, description="Plant carbonate weathering T and pCO2 factor"
  • VWmin (), VT_ReactProperty, description="Plant weighting for weathering T factors"
  • f_co2 (), VT_ReactProperty, description="Plant weighted silicate weathering T and pCO2 factor"
  • g_co2 (), VT_ReactProperty, description="Plant weighted carbonate weathering T and pCO2 factor"
  • w_plantenhance (), VT_ReactProperty, description="Plant weighted weathering rate factor"
  • silw (molC/yr), VT_ReactProperty, description="Silicate weathering"
  • carbw (molC/yr), VT_ReactProperty, description="Carbonate weathering"
  • oxw_fac (), VT_ReactProperty, description="Oxidative weathering oxygen-dependent factor"
  • oxidw (molC/yr), VT_ReactProperty, description="Oxidative organic C weathering"
  • gypw (molS/yr), VT_ReactProperty, description="Gypsum weathering"
  • pyrw (molS/yr), VT_ReactProperty, description="Pyrite weathering"
  • phosw_s (molP/yr), VT_ReactProperty, description="Phosphorus weathering, silicate-associated"
  • phosw_c (molP/yr), VT_ReactProperty, description="Phosphorus weathering, carbonate-associated"
  • phosw_o (molP/yr), VT_ReactProperty, description="Phosphorus weathering, organic carbon-associated"
  • phosw (molP/yr), VT_ReactProperty, description="Phosphorus weathering, total"
  • pland (molP/yr), VT_ReactProperty, description="Phosphorus weathering to land"
  • psea (molP/yr), VT_ReactProperty, description="Phosphorus weathering to sea"
  • ccdeg (molC/yr), VT_ReactProperty, description="Carbonate degassing"
  • ocdeg (molC/yr), VT_ReactProperty, description="Organic carbon degassing"
  • gypdeg (molS/yr), VT_ReactProperty, description="Gypsum degassing"
  • pyrdeg (molS/yr), VT_ReactProperty, description="Pyrite degassing"
  • Pconc (molP/kgsw), VT_ReactProperty, description="marine P conc"
  • Nconc (molN/kgsw), VT_ReactProperty, description="marine N conc"
  • newp (), VT_ReactProperty, description="marine new production"
  • ANOX (), VT_ReactProperty, description="marine anoxic fraction"
  • CPsea (), VT_ReactProperty, description="marine C:P ratio"
  • nfix (molN/yr), VT_ReactProperty, description="marine nitrogen fixation"
  • denit (molP/yr), VT_ReactProperty, description="marine denitrification"
  • mccb (molC/yr), VT_ReactProperty, description="Carbonate burial"
  • mocb (molC/yr), VT_ReactProperty, description="Marine organic carbon burial"
  • locb (molC/yr), VT_ReactProperty, description="Land organic carbon burial"
  • mopb (molP/yr), VT_ReactProperty, description="Marine organic P burial"
  • monb (molN/yr), VT_ReactProperty, description="Marine organic N burial"
  • capb (molP/yr), VT_ReactProperty, description="Marine carbonate-associated P burial"
  • fepb (molP/yr), VT_ReactProperty, description="Marine Fe-sorbed P burial"
  • mgsb (molS/yr), VT_ReactProperty, description="Marine gypsum sulphur burial"
  • mpsb (molS/yr), VT_ReactProperty, description="Marine pyrite sulphur burial"
• do_updatestate
  • P (mol), VT_ReactDependency, description="Marine phosphorus"
  • N (mol), VT_ReactDependency, description="Marine nitrogen"
  • O (mol), VT_ReactDependency, description="Atm-ocean oxygen"
  • C (mol), VT_ReactDependency, description="Sedimentary carbonate"
  • G (mol), VT_ReactDependency, description="Sedimentary organic carbon"
  • A (mol), VT_ReactDependency, description="Atm-ocean inorganic carbon"
  • CAL (mol), VT_ReactDependency, description="Marine calcium"
  • GYP (mol), VT_ReactDependency, description="Sedimentary gypsum"
  • PYR (mol), VT_ReactDependency, description="Sedimentary pyrite"
  • S (mol), VT_ReactDependency, description="Marine sulphate"
  • P_sms (mol yr-1), VT_ReactContributor, description="Marine phosphorus source-sinks"
  • N_sms (mol yr-1), VT_ReactContributor, description="Marine nitrogen source-sinks"
  • O_sms (mol yr-1), VT_ReactContributor, description="Atm-ocean oxygen source-sinks"
  • C_sms (mol yr-1), VT_ReactContributor, description="Sedimentary carbonate source-sinks"
  • G_sms (mol yr-1), VT_ReactContributor, description="Sedimentary organic carbon source-sinks"
  • A_sms (mol yr-1), VT_ReactContributor, description="Atm-ocean inorganic carbon source-sinks"
  • CAL_sms (mol yr-1), VT_ReactContributor, description="Marine calcium source-sinks"
  • GYP_sms (mol yr-1), VT_ReactContributor, description="Sedimentary gypsum source-sinks"
  • PYR_sms (mol yr-1), VT_ReactContributor, description="Sedimentary pyrite source-sinks"
  • S_sms (mol yr-1), VT_ReactContributor, description="Marine sulphate source-sinks"
  • P_norm (), VT_ReactDependency, description="normalized Marine phosphorus"
  • N_norm (), VT_ReactDependency, description="normalized Marine nitrogen"
  • O_norm (), VT_ReactDependency, description="normalized Atm-ocean oxygen"
  • C_norm (), VT_ReactDependency, description="normalized Sedimentary carbonate"
  • C_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary carbonate"
  • G_norm (), VT_ReactDependency, description="normalized Sedimentary organic carbon"
  • G_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary organic carbon"
  • A_norm (), VT_ReactDependency, description="normalized Atm-ocean inorganic carbon"
  • A_delta (per mil), VT_ReactDependency, description="isotope delta Atm-ocean inorganic carbon"
  • CAL_norm (), VT_ReactDependency, description="normalized Marine calcium"
  • GYP_norm (), VT_ReactDependency, description="normalized Sedimentary gypsum"
  • GYP_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary gypsum"
  • PYR_norm (), VT_ReactDependency, description="normalized Sedimentary pyrite"
  • PYR_delta (per mil), VT_ReactDependency, description="isotope delta Sedimentary pyrite"
  • S_norm (), VT_ReactDependency, description="normalized Marine sulphate"
  • S_delta (per mil), VT_ReactDependency, description="isotope delta Marine sulphate"
  • tforce (yr), VT_ReactDependency, description="time for external forcings"
  • SOLAR (W m-2), VT_ReactDependency, description="solar luminosity"
  • UPLIFT (), VT_ReactDependency, description="uplift scaling"
  • DEGASS (), VT_ReactDependency, description="degassing scaling"
  • W (), VT_ReactDependency, description="plant weathering scaling"
  • EVO (), VT_ReactDependency, description="plant evolution scaling"
  • Bforcing (), VT_ReactDependency, description="calcerous plankton evolution"
  • CPland_relative (), VT_ReactDependency, description="land CP burial ratio scaling"
  • TEMP (K), VT_ReactDependency, description="global temperature"
  • pO2PAL (), VT_ReactDependency, description="atmospheric oxygen relative to present-day"
  • pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 relative to present-day"
  • pCO2atm (atm), VT_ReactDependency, description="atmospheric pCO2"
  • d_mccb (per mil), VT_ReactDependency, description="D13C fractionation carbonate - atm-ocean inorganic carbon"
  • d_locb (per mil), VT_ReactDependency, description="D13C fractionation land organic carbon burial - atm-ocean inorganic carbon"
  • d_mocb (per mil), VT_ReactDependency, description="D13C fractionation marine organic carbon burial - atm-ocean inorganic carbon"
  • mccb_delta (per mil), VT_ReactDependency, description="D13C fractionation of marine calcium carbonate burial"
  • D_mpsb (per mil), VT_ReactDependency, description="D34S fractionation pyrite - marine sulphate"
  • V_T (), VT_ReactDependency, description="effect of temp on VEG"
  • V_co2 (), VT_ReactDependency, description="effect of CO2 on VEG"
  • V_o2 (), VT_ReactDependency, description="effect of O2 on VEG"
  • V_npp (), VT_ReactDependency, description="full VEG limitation"
  • mrO2 (), VT_ReactDependency, description="atmospheric O2 mixing ratio"
  • ignit (), VT_ReactDependency, description="ignition probability"
  • firef (), VT_ReactDependency, description="effect of fire on VEG"
  • VEG (), VT_ReactDependency, description="Mass of terrestrial biosphere"
  • f_preplant (), VT_ReactDependency, description="Pre-plant silicate weathering T and pCO2 factor"
  • f_plant (), VT_ReactDependency, description="Plant silicate weathering T and pCO2 factor"
  • g_preplant (), VT_ReactDependency, description="Pre-plant carbonate weathering T and pCO2 factor"
  • g_plant (), VT_ReactDependency, description="Plant carbonate weathering T and pCO2 factor"
  • VWmin (), VT_ReactDependency, description="Plant weighting for weathering T factors"
  • f_co2 (), VT_ReactDependency, description="Plant weighted silicate weathering T and pCO2 factor"
  • g_co2 (), VT_ReactDependency, description="Plant weighted carbonate weathering T and pCO2 factor"
  • w_plantenhance (), VT_ReactDependency, description="Plant weighted weathering rate factor"
  • silw (molC/yr), VT_ReactDependency, description="Silicate weathering"
  • carbw (molC/yr), VT_ReactDependency, description="Carbonate weathering"
  • oxw_fac (), VT_ReactDependency, description="Oxidative weathering oxygen-dependent factor"
  • oxidw (molC/yr), VT_ReactDependency, description="Oxidative organic C weathering"
  • gypw (molS/yr), VT_ReactDependency, description="Gypsum weathering"
  • pyrw (molS/yr), VT_ReactDependency, description="Pyrite weathering"
  • phosw_s (molP/yr), VT_ReactDependency, description="Phosphorus weathering, silicate-associated"
  • phosw_c (molP/yr), VT_ReactDependency, description="Phosphorus weathering, carbonate-associated"
  • phosw_o (molP/yr), VT_ReactDependency, description="Phosphorus weathering, organic carbon-associated"
  • phosw (molP/yr), VT_ReactDependency, description="Phosphorus weathering, total"
  • pland (molP/yr), VT_ReactDependency, description="Phosphorus weathering to land"
  • psea (molP/yr), VT_ReactDependency, description="Phosphorus weathering to sea"
  • ccdeg (molC/yr), VT_ReactDependency, description="Carbonate degassing"
  • ocdeg (molC/yr), VT_ReactDependency, description="Organic carbon degassing"
  • gypdeg (molS/yr), VT_ReactDependency, description="Gypsum degassing"
  • pyrdeg (molS/yr), VT_ReactDependency, description="Pyrite degassing"
  • Pconc (molP/kgsw), VT_ReactDependency, description="marine P conc"
  • Nconc (molN/kgsw), VT_ReactDependency, description="marine N conc"
  • newp (), VT_ReactDependency, description="marine new production"
  • ANOX (), VT_ReactDependency, description="marine anoxic fraction"
  • CPsea (), VT_ReactDependency, description="marine C:P ratio"
  • nfix (molN/yr), VT_ReactDependency, description="marine nitrogen fixation"
  • denit (molP/yr), VT_ReactDependency, description="marine denitrification"
  • mccb (molC/yr), VT_ReactDependency, description="Carbonate burial"
  • mocb (molC/yr), VT_ReactDependency, description="Marine organic carbon burial"
  • locb (molC/yr), VT_ReactDependency, description="Land organic carbon burial"
  • mopb (molP/yr), VT_ReactDependency, description="Marine organic P burial"
  • monb (molN/yr), VT_ReactDependency, description="Marine organic N burial"
  • capb (molP/yr), VT_ReactDependency, description="Marine carbonate-associated P burial"
  • fepb (molP/yr), VT_ReactDependency, description="Marine Fe-sorbed P burial"
  • mgsb (molS/yr), VT_ReactDependency, description="Marine gypsum sulphur burial"
  • mpsb (molS/yr), VT_ReactDependency, description="Marine pyrite sulphur burial"

ReactionCIsotopes

Carbon isotope fractionation from Bergman (2004) COPSE biogeochemical model.

Calculates global mean isotope fractionation for marine carbonate burial and land and ocean organic carbon burial from global mean TEMP, pCO2PAL and pO2PAL.

Parameters

• do_D_mccb_DIC[Bool]=true, default_value=true, description="provide marine calcite burial relative to ocean DIC"
• do_D_B_mccb_mocb[Bool]=true, default_value=true, description="provide fractionation between marine organic and calcite burial"
• do_D_P_CO2_locb[Bool]=true, default_value=true, description="provide fractionation between terrestrial organic burial and atmospheric CO2"
• f_cisotopefrac[String]="copse_base", default_value="copse_base", allowed_values=["fixed", "copsebase", "copsenoO2"], description="fractionation calculation method"

Methods and Variables for default Parameters

• do_CIsotopes
  • D_eqbw_CO2 –> land.D_eqbw_CO2 (per mil), VT_ReactProperty, description="d13C fractionation between atmospheric CO2 and fresh water"
  • D_mccb_DIC –> ocean.D_mccb_DIC (per mil), VT_ReactProperty, description="d13C marine calcite burial relative to ocean DIC"
  • D_B_mccb_mocb –> ocean.D_B_mccb_mocb (per mil), VT_ReactProperty, description="d13C fractionation between marine organic and calcite burial"
  • D_P_CO2_locb –> land.D_P_CO2_locb (per mil), VT_ReactProperty, description="d13C fractionation between terrestrial organic burial and atmospheric CO2"
  • pCO2PAL –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 normalized to present day"
  • TEMP (K), VT_ReactDependency, description="global surface temperature"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric pO2 normalized to present day"

ReactionAtmOcean_O

Combined atmosphere + ocean scalar O (oxygen) reservoir for use with COPSE model.

Provides:

• state variable O (O2 in mol) or O_solve (O2 normalized by O:norm_value attribute)
• state variable time derivative O_sms (mol yr-1) or O_solve_sms (yr-1)
• O_norm (O normalized by O:norm_value attribute, which should be set in .yaml config file to present-day atmospheric value).

Also calculates additional quantities pO2atm (partial pressure in bar), and pO2PAL (equal to O_norm), which should usually be relinked to the atm Domain in the config file. Assumes ocean oxygen is a neglible fraction of the total.

Parameters

• const[Bool]=false, default_value=false, description="true to provide constant value, ignoring fluxes from _sms Variable"
• state_norm[Bool]=false, default_value=false, description="true to provide solver with normalized values O_solve and O_solve_sms"

Methods and Variables

• methodfn_do_nothing
  • O_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="atm-ocean oxygen source-sinks"
• do_AtmOcean_O
  • O_norm (), VT_ReactProperty, description="atm-ocean normalized"
  • pO2atm (atm), VT_ReactProperty, description="atmospheric pO2"
  • pO2PAL (), VT_ReactProperty, description="atmospheric pO2 normalized to present day"
  • O (mol), VT_ReactDependency, VF_StateExplicit, description="atm-ocean oxygen"

ReactionAtmOcean_A

Atmosphere-ocean inorganic carbon A reservoir, for use with the COPSE model.

Provides:

• state variable A (total C in atmospheric CO2 and ocean DIC, in moles), or A_solve (normalized by A:norm_value attribute)
• state variable time derivative A_sms (mol yr-1) or A_solve_sms (yr-1)
• A_norm (A normalized by A:norm_value attribute, which should be set in .yaml config file to the pre-industrial value of 3.193e18 mol).

Also calculates partitioning into atmosphere and ocean (atm-ocean fraction phi) and atmospheric pCO2atm (partial pressure in bar), and pCO2PAL, which should usually be relinked to the atm Domain in the config file.

The calculation of phi atm-ocean fraction is set by Parameter f_atfrac:

• original: fixed phi, as used in the original COPSE model (Bergman et al., 2004).
• quadratic: phi proportional to A, approximating the behaviour of the carbonate system assuming carbonate saturation hence [CO3--] carbonate ion concentration is approximately constant.

If Parameter delta_atm_ocean == true, also calculates atmosphere CO2 and ocean DIC isotopic fractionation.

Parameters

• f_atfrac[String]="original", default_value="original", allowed_values=["original", "quadratic"], description="atm-ocean partitioning"
• delta_atm_ocean[Bool]=true, default_value=true, description="calculate d13CO2, d13DIC relative to A"
• fix_cisotopefrac_T[Bool]=false, default_value=false, description="remove temperature dependence of d13CO2, d13DIC relative to A"
• const[Bool]=false, default_value=false, description="true to provide constant value, ignoring fluxes from _sms Variable"
• state_norm[Bool]=false, default_value=false, description="true to provide solver with normalized values A_solve and A_solve_sms"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables

• methodfn_do_nothing
  • A_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="atm-ocean inorganic carbon (CO2 + DIC) source-sinks"
• do_AtmOcean_A
  • A_norm (), VT_ReactProperty, description="atm-ocean inorganic carbon (CO2 + DIC) normalized to present day"
  • pCO2atm (atm), VT_ReactProperty, description="atmospheric pCO2"
  • pCO2PAL (), VT_ReactProperty, description="atmospheric pCO2 normalized to present day"
  • phi (), VT_ReactProperty, description="atmospheric pCO2 fraction"
  • A (mol), VT_ReactDependency, VF_StateExplicit, description="atm-ocean inorganic carbon (CO2 + DIC)"

ReactionGlobalTemperatureCK1992

Global temperature iterative calculation from SOLAR forcing, pCO2atm. Provides a TEMP state variable, with either an error term for a DAE solver (if temp_DAE = true), or a restoring term for an ODE solver (if temp_DAE = false).

Valid range: 1e-8 < pCO2atm < 1e-2 (bar), 273.15 < TEMP < 283.15 (K)

Parameters

• fixed_albedo[Float64]=NaN, default_value=NaN, description="NaN to calculate albedo, value in range (0.0 - 1.0) to fix albedo"
• tempcorrect[Float64]=0.194 (K), default_value=0.194, description="COPSE temp correction to 15C at present day"
• temp_DAE[Bool]=false, default_value=false, description="solve TEMP as an algebraic constraint (requires DAE solver"

Methods and Variables

• do_GlobalTemperatureCK1992
  • pCO2atm –> atm.pCO2atm (atm), VT_ReactDependency, description="atmospheric CO2 partial pressure"
  • SOLAR (W m-2), VT_ReactDependency, description="incident solar radiation at Earth"
  • albedo (), VT_ReactProperty, description="planetary albedo"
  • Teff (K), VT_ReactProperty, description="black body effective temperature"
  • Tgreenhouse (K), VT_ReactProperty, description=""
  • TEMP (K), VT_ReactDependency, VF_StateExplicit, description="global surface temperature"
  • TEMP_sms (K yr-1), VT_ReactContributor, VF_Deriv, description="rate of change of global surface temperature"

ReactionGlobalTemperatureBerner

Global temperature calculation from pCO2, with implicit change in solar luminosity (calculated from forcing time tforce).

Parameters

• k_c[Float64]=4.328 (K), default_value=4.328, description="climate sensitivity to CO2"
• k_l[Float64]=7.4 (K (570e6 yr)-1), default_value=7.4, description="rate of change of solar luminosity"

Methods and Variables

• do_GlobalTemperatureBerner
  • TEMP (K), VT_ReactProperty, description="global surface temperature"
  • pCO2PAL –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric CO2 partial pressure relative to pre-industrial"
  • tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"

Strontium

Strontium system with 87Sr/86Sr.

Based on (Francois and Walker, 1992). This implementation is described in (Mills et al., 2014), (Lenton et al., 2018).

A Sr model configuration should contain the following Reservoirs and Reactions:

ReactionSrMantleCrust

Calculate strontium isotope composition of mantle, old (granite), and new (basalt) igneous rocks as a function of time, given present day isotopic composition and an initial uniform value at the formation of the Earth. Assumes all subsequent evolution was due to Rb decay with different Rb/Sr ratios (ie no exchange between these mantle and rock reserovirs).

Parameters

• Sr_delta_0[Float64]=0.69898, default_value=0.69898, description="uniform d78Sr isotopic fractionation at formation of Earth"
• lambda_Rb[Float64]=1.4e-11 (yr-1), default_value=1.4e-11, description="Rb decay rate to 87Sr"
• Sr_old_ig_delta_present[Float64]=NaN, default_value=NaN, description="present-day d78Sr isotopic composition of old igneous rocks (granite)"
• Sr_new_ig_delta_present[Float64]=NaN, default_value=NaN, description="present-day d78Sr isotopic composition of new igneous rocks (basalt)"
• Sr_mantle_delta_present[Float64]=NaN, default_value=NaN, description="present-day d78Sr isotopic composition of mantle"

Methods and Variables

• do_Sr_mantle_crust
  • tforce –> global.tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • Sr_old_ig_delta (unknown), VT_ReactProperty, description="d87Sr old igneous rocks (granite)"
  • Sr_new_ig_delta (unknown), VT_ReactProperty, description="d87Sr new igneous rocks (basalt)"
  • Sr_mantle_delta (unknown), VT_ReactProperty, description="d87Sr mantle"

ReactionSrSed

Calculate contribution to rate of change of a sedimentary Sr_sed reservoir due to metamorphic loss, and Rb decay.

Parameters

• lambda_Rb[Float64]=1.4e-11 (yr-1), default_value=1.4e-11, description="Rb decay rate to 87Sr"
• sediment_RbSr[Float64]=0.5, default_value=0.5, description="present-day sediment Rb:Sr ratio"
• f_Sr_metam[String]="alternative", default_value="alternative", allowed_values=["original", "alternative"], description="functional form for sediment Sr metamorphic loss"
• k_Sr_metam[Float64]=1.3e10 (mol yr-1), default_value=1.3e10, description="rate of metamorphic loss of Sr from sedimentary reservoir"
• SrIsotope[external, UnionAll]=PALEOboxes.IsotopeLinear, default_value=PALEOboxes.IsotopeLinear, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable Sr isotopes and specify isotope type"

Methods and Variables

• do_Sr_sed
  • tforce –> global.tforce (yr), VT_ReactDependency, description="historical time at which to apply forcings, present = 0 yr"
  • DEGASS –> global.DEGASS (), VT_ReactDependency, description="normalized DEGASS forcing"
  • Sr_sed (mol), VT_ReactDependency, description="sedimentary Sr"
  • Sr_sed_delta (unknown), VT_ReactDependency, description="d87Sr of sedimentary Sr"
  • Sr_sed_norm (), VT_ReactDependency, description="normalized sedimentary Sr"
  • Sr_sed_sms (mol yr-1), VT_ReactContributor, description="sedimentary Sr source minus sink flux"

ReactionSrLand

Calculate Sr weathering flux from land surface, given relative (normalized) basalt, granite, carbonate weathering rates and Sr isotopic composition.

Parameters

• k_Sr_total_igw[Float64]=1.3e10 (mol yr-1), default_value=1.3e10, description="total Sr weathering rate constant from igneous rocks (granite + basalt). NB: only used during configuration!!"
• k_Sr_basw[Float64]=NaN (mol yr-1), default_value=NaN, description="Sr basalt weathering rate constant"
• k_Sr_granw[Float64]=NaN (mol yr-1), default_value=NaN, description="Sr granite weathering rate constant from granite"
• f_Sr_sedw[String]="alternative", default_value="alternative", allowed_values=["original", "alternative"], description="functional form for sediment Sr weathering"
• k_Sr_sedw[Float64]=1.7e10 (mol yr-1), default_value=1.7e10, description="Sr weathering rate constant from sediments"
• SrIsotope[external, UnionAll]=PALEOboxes.IsotopeLinear, default_value=PALEOboxes.IsotopeLinear, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable Sr isotopes and specify isotope type"

Methods and Variables

• do_Sr_land
  • basw_relative (), VT_ReactDependency, description="Basalt weathering normalized to present"
  • granw_relative (), VT_ReactDependency, description="Granite weathering normalized to present"
  • carbw_relative (), VT_ReactDependency, description="Carbonate weathering normalized to present"
  • fluxRtoOcean_Sr –> fluxRtoOcean.flux_Sr (mol yr-1), VT_ReactContributor, description="Sr riverine flux"
  • fluxLandtoSedCrust_Sr –> fluxLandtoSedCrust.flux_Sr (mol yr-1), VT_ReactContributor, description="Sr flux from land to sedimentary reservoirs"
  • Sr_old_ig_delta –> sedcrust.Sr_old_ig_delta (unknown), VT_ReactDependency, description="d87Sr old igneous rocks (granite)"
  • Sr_new_ig_delta –> sedcrust.Sr_new_ig_delta (unknown), VT_ReactDependency, description="d87Sr new igneous rocks (basalt)"
  • Sr_sed_delta –> sedcrust.Sr_sed_delta (unknown), VT_ReactDependency, description="d87Sr of sedimentary Sr"
  • Sr_sed_norm –> sedcrust.Sr_sed_norm (), VT_ReactDependency, description="normalized sedimentary Sr"

ReactionSrOceanfloor

Calculate evolution of an oceanSr reservoir due to ocean burial (assumed proportional to carbonate burial), seafloor weathering, and hydrothermal (mantle) input fluxes.

Parameters

• k_Sr_mantle[Float64]=7.3e9 (mol yr-1), default_value=7.3e9, description="Sr mantle (hydrothermal) input"
• k_Sr_sfw[Float64]=NaN (mol yr-1), default_value=NaN, description="Sr seafloor weathering output"
• f_Sr_sedb[String]="carbburial", default_value="carbburial", allowed_values=["carbburial", "silwcarbw"], description="functional form for Sr burial"
• k_Sr_sedb[Float64]=NaN (mol yr-1), default_value=NaN, description="Sr burial output"
• k_mccb_0[Float64]=NaN (mol yr-1), default_value=NaN, description="Carbonate burial rate to normalize Sr burial output for f_Sr_sedb="carbburial""
• SrIsotope[external, UnionAll]=PALEOboxes.IsotopeLinear, default_value=PALEOboxes.IsotopeLinear, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable Sr isotopes and specify isotope type"

Methods and Variables

• do_Sr_oceanfloor
  • DEGASS –> global.DEGASS (), VT_ReactDependency, description="normalized DEGASS forcing"
  • silwcarbw_relative –> land.silwcarbw_relative (), VT_ReactDependency, description="normalized land silicate+carbonate weathering"
  • sfw_relative (), VT_ReactDependency, description="normalized seafloor weathering"
  • solutefluxOceanfloor_Sr –> fluxOceanfloor.soluteflux_Sr (mol yr-1), VT_ReactContributor, description="Sr oceanfloor solute flux"
  • fluxOceanBurial_Sr –> fluxOceanBurial.flux_Sr (mol yr-1), VT_ReactContributor, description="Sr ocean burial flux"
  • fluxOceanBurial_Ccarb –> fluxOceanBurial.flux_Ccarb (mol yr-1), VT_ReactDependency, description="carbonate ocean burial flux"
  • Sr_norm –> ocean.Sr_norm (), VT_ReactDependency, description="normalized ocean Sr"
  • Sr_delta –> ocean.oceanfloor.Sr_delta (unknown), VT_ReactDependency, description="ocean d87Sr"
  • Sr_mantle_delta –> sedcrust.Sr_mantle_delta (unknown), VT_ReactDependency, description="mantle d87Sr"

ReactionLandBergman2004

COPSE Bergman(2004) land surface

Parameters

• k5_locb[Float64]=4.5e12 (mol/yr), default_value=4.5e12, description="land organic carbon burial"
• k11_landfrac[Float64]=0.10345, default_value=0.10345, description="fract of weath P buried on land"
• k14_carbw[Float64]=1.335e13 (mol/yr), default_value=1.335e13, description="carbonate weathering"
• k15_plantenhance[Float64]=0.15, default_value=0.15, description="weathering enhancement factor prior to vascular plant colonisation"
• k_fire[Float64]=100.0, default_value=100.0, description="fire feedback"
• k16_PANtoO[Float64]=3.762, default_value=3.762, description="For calculating mixing ratio O2 from normalised O2"
• k_silw[Float64]=NaN (mol/yr), default_value=NaN, description="silicate weathering"
• k10_phosw[Float64]=NaN (mol/yr), default_value=NaN, description="phosphorus weathering"
• k17_oxidw[Float64]=NaN (mol/yr), default_value=NaN, description="oxidative org carbon weathering"
• enableS[Bool]=true, default_value=true, description="enable S weathering"
• k21_pyrw[Float64]=5.3e11 (mol S/yr), default_value=5.3e11, description="pyrite weathering"
• k22_gypw[Float64]=1.0e12 (mol S/yr), default_value=1.0e12, description="gypsum weathering"
• f_carbwC[String]="Cindep", default_value="Cindep", allowed_values=["Cindep", "Cprop"], description="C (carbonate reservoir) dependence of carbonate weathering"
• f_oxwO[String]="PowerO2", default_value="PowerO2", allowed_values=["PowerO2", "SatO2"], description="oxidative weathering functional form"
• f_oxw_a[Float64]=0.5, default_value=0.5, description="oxidative weathering dependency on O2 concentration"
• f_landbiota[String]="Dynamic", default_value="Dynamic", allowed_values=["Dynamic", "Prescribed"], description="enable/disable dynamic land biota (VEG required as forcing if Prescribed)"
• f_locb[String]="original", default_value="original", allowed_values=["original", "Prescribed"], description=""
• dic_runoff[Bool]=true, default_value=true, description="true to add additional DIC runoff terms to riverine (and atmosphere) fluxes so riverine DIC ~ TAlk, false to just use riverine DIC = 'carbw'"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
• SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_land_bergman2004
  • fluxAtoLand_flux_CO2 –> fluxAtoLand.flux_CO2 (mol yr-1), VT_ReactContributor, description="flux CO2"
  • fluxAtoLand_flux_O2 –> fluxAtoLand.flux_O2 (mol yr-1), VT_ReactContributor, description="flux O2"
  • fluxRtoOcean_flux_DIC –> fluxRtoOcean.flux_DIC (mol yr-1), VT_ReactContributor, description="flux DIC"
  • fluxRtoOcean_flux_TAlk –> fluxRtoOcean.flux_TAlk (mol yr-1), VT_ReactContributor, description="flux TAlk"
  • fluxRtoOcean_flux_Ca –> fluxRtoOcean.flux_Ca (mol yr-1), VT_ReactContributor, description="flux Ca"
  • fluxRtoOcean_flux_P –> fluxRtoOcean.flux_P (mol yr-1), VT_ReactContributor, description="flux P"
  • fluxRtoOcean_flux_SO4 –> fluxRtoOcean.flux_SO4 (mol yr-1), VT_ReactContributor, description="flux SO4"
  • fluxLandtoSedCrust_flux_Ccarb –> fluxLandtoSedCrust.flux_Ccarb (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • fluxLandtoSedCrust_flux_Corg –> fluxLandtoSedCrust.flux_Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
  • fluxLandtoSedCrust_flux_GYP –> fluxLandtoSedCrust.flux_GYP (mol yr-1), VT_ReactContributor, description="flux GYP"
  • fluxLandtoSedCrust_flux_PYR –> fluxLandtoSedCrust.flux_PYR (mol yr-1), VT_ReactContributor, description="flux PYR"
  • VEG (), VT_ReactProperty, description="Mass of terrestrial biosphere"
  • tforce –> global.tforce (yr), VT_ReactDependency, description="time for external forcings"
  • UPLIFT –> global.UPLIFT (), VT_ReactDependency, description="uplift scaling"
  • W –> global.W (), VT_ReactDependency, description="plant weathering scaling"
  • [EVO] –> global.EVO (), VT_ReactDependency, description="plant evolution scaling"
  • [CPland_relative] –> global.CPland_relative (), VT_ReactDependency, description="land CP burial ratio scaling"
  • [locbpert] –> global.locbpert (), VT_ReactDependency, description="land organic carbon burial forcing (f_locb==Prescribed only)"
  • TEMP –> global.TEMP (K), VT_ReactDependency, description="global temperature"
  • [D_P_CO2_locb] (per mil), VT_ReactDependency, description="d13C fractionation between terrestrial organic burial and atmospheric CO2"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric oxygen relative to present-day"
  • pCO2PAL –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 relative to present-day"
  • pCO2atm –> atm.pCO2atm (atm), VT_ReactDependency, description="atmospheric pCO2"
  • [CO2_delta] –> atm.CO2_delta (per mil), VT_ReactDependency, description="atmospheric pCO2 delta 13C"
  • C_norm –> sedcrust.C_norm (), VT_ReactDependency, description="Sedimentary carbonate normalized to present day"
  • [C_delta] –> sedcrust.C_delta (per mil), VT_ReactDependency, description="Sedimentary carbonate d13C"
  • G_norm –> sedcrust.G_norm (), VT_ReactDependency, description="Sedimentary organic carbon normalized to present day"
  • [G_delta] –> sedcrust.G_delta (per mil), VT_ReactDependency, description="Sedimentary organic carbon d13C"
  • [GYP_norm] –> sedcrust.GYP_norm (), VT_ReactDependency, description="Sedimentary gypsum normalized to present day"
  • [GYP_delta] –> sedcrust.GYP_delta (per mil), VT_ReactDependency, description="Sedimentary gypsum d34S"
  • [PYR_norm] –> sedcrust.PYR_norm (), VT_ReactDependency, description="Sedimentary pyrite normalized to present day"
  • [PYR_delta] –> sedcrust.PYR_delta (per mil), VT_ReactDependency, description="Sedimentary pyrite d34S"
  • V_T (), VT_ReactProperty, description="effect of temp on VEG"
  • V_co2 (), VT_ReactProperty, description="effect of CO2 on VEG"
  • V_o2 (), VT_ReactProperty, description="effect of O2 on VEG"
  • V_npp (), VT_ReactProperty, description="full VEG limitation"
  • mrO2 (), VT_ReactProperty, description="atmospheric O2 mixing ratio"
  • ignit (), VT_ReactProperty, description="ignition probability"
  • firef (), VT_ReactProperty, description="effect of fire on VEG"
  • f_preplant (), VT_ReactProperty, description="Pre-plant silicate weathering T and pCO2 factor"
  • f_plant (), VT_ReactProperty, description="Plant silicate weathering T and pCO2 factor"
  • g_preplant (), VT_ReactProperty, description="Pre-plant carbonate weathering T and pCO2 factor"
  • g_plant (), VT_ReactProperty, description="Plant carbonate weathering T and pCO2 factor"
  • VWmin (), VT_ReactProperty, description="Plant weighting for weathering T factors"
  • f_co2 (), VT_ReactProperty, description="Plant weighted silicate weathering T and pCO2 factor"
  • g_co2 (), VT_ReactProperty, description="Plant weighted carbonate weathering T and pCO2 factor"
  • w_plantenhance (), VT_ReactProperty, description="Plant weighted weathering rate factor"
  • silw (molC/yr), VT_ReactProperty, description="Silicate weathering"
  • silw_relative (), VT_ReactProperty, description="Silicate weathering normalized to present day"
  • carbw (molC/yr), VT_ReactProperty, description="Carbonate weathering"
  • carbw_relative (), VT_ReactProperty, description="Carbonate weathering normalized to present day"
  • oxw_fac (), VT_ReactProperty, description="Oxidative weathering oxygen-dependent factor"
  • oxidw (molC/yr), VT_ReactProperty, description="Oxidative organic C weathering"
  • oxidw_relative (), VT_ReactProperty, description="Oxidative organic C weathering normalized to present day"
  • gypw (molS/yr), VT_ReactProperty, description="Gypsum weathering"
  • pyrw (molS/yr), VT_ReactProperty, description="Pyrite weathering"
  • phosw_s (molP/yr), VT_ReactProperty, description="Phosphorus weathering, silicate-associated"
  • phosw_c (molP/yr), VT_ReactProperty, description="Phosphorus weathering, carbonate-associated"
  • phosw_o (molP/yr), VT_ReactProperty, description="Phosphorus weathering, organic carbon-associated"
  • phosw (molP/yr), VT_ReactProperty, description="Phosphorus weathering, total"
  • pland (molP/yr), VT_ReactProperty, description="Phosphorus weathering to land"
  • psea (molP/yr), VT_ReactProperty, description="Phosphorus weathering to sea"
  • locb (molC/yr), VT_ReactProperty, description="Land organic carbon burial"
  • locb_delta (per mil), VT_ReactProperty, description="Land organic carbon burial d13C"
  • eps_eqbw (per mil), VT_ReactProperty, description="approximate atmosphere-runoff d13C"

ReactionLandArea

Calculate land areas and lithology.

Provides GRAN_AREA and BA_AREA.

Parameters

• f_granitearea[String]="Fixed", default_value="Fixed", allowed_values=["Fixed", "Forced", "OrgEvapForced"], description="Granite area function"
• orgevapfrac[Float64]=0.6, default_value=0.6, description="weighting for f_granitearea OrgEvapForced option"
• f_basaltarea[String]="Fixed", default_value="Fixed", allowed_values=["Fixed", "Forced", "g32014constructfromlips"], description="Basalt area function"
• present_basalt_area[Float64]=6.8e6 (km^2), default_value=6.8e6, description="Present basalt area including island basalts, CFBs"
• oib_area_scaling[Float64]=2.0e6 (km^2), default_value=2.0e6, description="Scaling factor to calculate ocean island basalt area from normalized DEGASS forcing"

Methods and Variables for default Parameters

• do_land_area
  • GRAN_AREA (), VT_ReactProperty, description="Granite area normalized to present day"
  • BA_AREA (), VT_ReactProperty, description="Basalt area normalized to present day"

ReactionLandBiota

COPSE Reloaded(2018) land biota. Calculates VEG, representing land plant coverage and biomass.

In a scalar (0D) Domain, this functions as in COPSE to calculate a global mean.

In a spatially-resolved Domain, this calculates local properties using local TEMP.

Parameters

• f_npp[String]="original", default_value="original", allowed_values=["original", "noT", "noO2", "noCO2", "bernerCO2", "newCO2", "constant"], description="functional form for VEG limitation by EVO, temperature, O2, CO2"
• k16_PANtoO[Float64]=3.762, default_value=3.762, description="For calculating mixing ratio O2 from normalised O2"
• f_ignit[String]="original", default_value="original", allowed_values=["original", "bookchapter", "nofbk"], description="functional form for fire feedback"
• k_fire[Float64]=100.0, default_value=100.0, description="fire feedback"

Methods and Variables for default Parameters

• do_land_biota
  • EVO –> global.EVO (), VT_ReactDependency, description="plant evolution scaling"
  • [fireforcing] –> global.fireforcing (), VT_ReactDependency, description="optional fireforcing"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric oxygen relative to present-day"
  • pCO2PAL –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 relative to present-day"
  • pCO2atm –> atm.pCO2atm (atm), VT_ReactDependency, description="atmospheric pCO2"
  • TEMP –> global.TEMP (K), VT_ReactDependency, description="global or local temperature"
  • V_co2 (), VT_ReactProperty, description="effect of CO2 on VEG"
  • V_o2 (), VT_ReactProperty, description="effect of O2 on VEG"
  • mrO2 (), VT_ReactProperty, description="atmospheric O2 mixing ratio"
  • ignit (), VT_ReactProperty, description="ignition probability"
  • firef (), VT_ReactProperty, description="effect of fire on VEG"
  • V_T (), VT_ReactProperty, description="effect of temp on VEG"
  • V_npp (), VT_ReactProperty, description="full VEG limitation"
  • VEG (), VT_ReactProperty, description="Mass of terrestrial biosphere"

ReactionLandWeatheringRates

COPSE Reloaded(2018) weathering rates. Calculates weathering rates as a function of temperature, pCO2, pO2 and biosphere VEG and biological weathering enhancement W.

In a scalar (0D) Domain, this functions as in COPSE to calculate global mean rates.

In a spatially-resolved Domain, this calculates local rates (use 'f_runoff' parameter to choose an appropriate hydrological parameterisation based on a supplied spatially-varying runoff (kg m-2 s-1)).

Parameters

• f_act_energies[String]="single", default_value="single", allowed_values=["single", "split"], description="weathering kinetics for granite and basalt"
• f_runoff[String]="original", default_value="original", allowed_values=["original", "geoclim2004", "linearrunoff"], description="runoff dependency of weathering"
• k_runoff_mean[Float64]=3.0e-5 (kg m-2 s-1), default_value=3.0e-5, description="global mean runoff (f_runoff != original only)"
• k_runoff_freeze[Float64]=0.0 (K), default_value=0.0, description="local temperature below which weathering is zero (f_runoff != original only)"
• f_co2fert[String]="original", default_value="original", allowed_values=["original", "geocarb3", "off"], description="CO2 and O2 dependence of plant effects on CO2 weathering"
• f_oxwO[String]="PowerO2", default_value="PowerO2", allowed_values=["PowerO2", "IndepO2"], description="functional form for oxygen sensitivity of oxidative weathering"
• f_oxw_a[Float64]=0.5, default_value=0.5, description="power law dependence of oxidative weathering oxygen sensitivity"
• k15_plantenhance[Float64]=0.15, default_value=0.15, description="weathering enhancement factor prior to vascular plant colonisation"
• f_vegweath[String]="original", default_value="original", allowed_values=["original", "new", "new2", "newnpp"], description="vegetation dependence of silicate,carbonate weathering"

Methods and Variables for default Parameters

• do_land_weathering_rates
  • W –> global.W (), VT_ReactDependency, description="biological enhancement of weathering"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric oxygen relative to present-day"
  • pCO2PAL –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2 relative to present-day"
  • TEMP –> global.TEMP (K), VT_ReactDependency, description="global or local temperature"
  • [runoff] (kg m-2 s-1), VT_ReactDependency, description="runoff"
  • [V_npp] (), VT_ReactDependency, description="full VEG limitation"
  • VEG (), VT_ReactDependency, description="Mass of terrestrial biosphere"
  • f_CO2_abiotic (), VT_ReactProperty, description="abiotic CO2 dependence of carbonate silicate weathering"
  • f_CO2_biotic (), VT_ReactProperty, description="biotic CO2 dependence of carbonate silicate weathering"
  • oxw_facO (), VT_ReactProperty, description="oxidative weathering oxygen dependence factor"
  • oxw_facOmax (), VT_ReactProperty, description="maximum possible oxidative weathering factor at high pO2"
  • f_T_gran (), VT_ReactProperty, description="granite T dependence from activation energy"
  • f_T_bas (), VT_ReactProperty, description="basalt T dependence from activation energy"
  • f_T_ap (), VT_ReactProperty, description="apatite T dependence from activation energy"
  • f_T_runoff (), VT_ReactProperty, description="runoff silicate temperature dependence"
  • g_T_runoff (), VT_ReactProperty, description="runoff carbonate temperature dependence"
  • f_gran (), VT_ReactProperty, description="granite weathering rate"
  • f_bas (), VT_ReactProperty, description="basalt weathering rate"
  • f_ap (), VT_ReactProperty, description="apatite weathering rate"
  • f_carb (), VT_ReactProperty, description="carbonate weathering rate"
  • VWmin (), VT_ReactProperty, description="VEG (biosphere) and W (evolutionary) weathering factor"

ReactionLandWeatheringFluxes

COPSE Reloaded(2018) weathering fluxes. Calculates and applies global weathering fluxes and land burial given weathering rates and land areas.

Fluxes are added to flux couplers:

• fluxAtoLand: CO2 and O2 exchange with atmosphere
• fluxRtoOcean: riverine fluxes
• fluxLandtoSedCrust: sedimentary reservoir weathering and land organic carbon burial

Parameters

• f_gran_link_u[String]="original", default_value="original", allowed_values=["original", "weak", "none"], description="granite weathering uplift dependence"
• f_bas_link_u[String]="yes", default_value="yes", allowed_values=["yes", "weak", "no"], description="basalt weathering uplift dependence"
• k_basfrac[Float64]=0.35, default_value=0.35, description="fraction of silicate weathering that is basaltic at present"
• k_granw[Float64]=NaN (mol/yr), default_value=NaN, description="granite weathering rate"
• k_basw[Float64]=NaN (mol/yr), default_value=NaN, description="basalt weathering rate"
• f_p_kinetics[String]="no", default_value="no", allowed_values=["no", "yes"], description="apatite kinetics independent of host rock"
• f_p_apportion[String]="no", default_value="no", allowed_values=["no", "yes"], description="P content vary between granite and basalt"
• k_P[Float64]=2.15, default_value=2.15, description="enrichment P:(Ca+Mg) in granite vs basalt "
• k10_phosw[Float64]=NaN (mol/yr), default_value=NaN, description="phosphorus weathering"
• k_Psilw[Float64]=0.16666666666666666, default_value=0.16666666666666666, description="fraction of P weathering from silicates"
• k_Pcarbw[Float64]=0.4166666666666667, default_value=0.4166666666666667, description="fraction of P weathering associated with carbonates"
• k_Poxidw[Float64]=0.4166666666666667, default_value=0.4166666666666667, description="fraction of P weathering from organic matter"
• k_Psedw[Float64]=0.0, default_value=0.0, description="fraction of P weathering from other sedimentary rocks"
• f_carb_link_u[String]="yes", default_value="yes", allowed_values=["yes", "no"], description="carbonate weathering uplift dependence"
• f_carbwC[String]="Cindep", default_value="Cindep", allowed_values=["Cindep", "Cprop"], description="C (carbonate reservoir) dependence of carbonate weathering"
• k14_carbw[Float64]=1.335e13 (mol/yr), default_value=1.335e13, description="carbonate weathering"
• f_oxwG[String]="Gprop", default_value="Gprop", allowed_values=["Gindep", "Gprop", "forced"], description="G (organic carbon reservoir) dependence of oxidative weathering"
• k17_oxidw[Float64]=NaN (mol/yr), default_value=NaN, description="oxidative org carbon weathering"
• enableS[Bool]=true, default_value=true, description="enable S weathering"
• f_pyrweather[String]="copse_O2", default_value="copse_O2", allowed_values=["copseO2", "copsenoO2", "forced"], description="functional form of dependence of pyrite weathering"
• k21_pyrw[Float64]=5.3e11 (mol S/yr), default_value=5.3e11, description="pyrite weathering"
• f_gypweather[String]="original", default_value="original", allowed_values=["original", "alternative", "forced"], description="functional form of dependence of gypsum weathering"
• k22_gypw[Float64]=1.0e12 (mol S/yr), default_value=1.0e12, description="gypsum weathering"
• SRedoxAlk[Bool]=false, default_value=false, description="true to include -TAlk from pyrite weathering"
• f_locb[String]="original", default_value="original", allowed_values=["original", "Uforced", "coal", "split", "Prescribed"], description="functional form of dependence of land organic carbon burial"
• k5_locb[Float64]=4.5e12 (mol/yr), default_value=4.5e12, description="land organic carbon burial (f_locb==Prescribed only)"
• k11_landfrac[Float64]=0.10345, default_value=0.10345, description="fract of weath P buried on land"
• k_aq[Float64]=0.8, default_value=0.8, description="fraction of locb assumed to occur in aquatic settings (not coals)"
• CPland0[Float64]=1000.0, default_value=1000.0, description="present-day C/P land burial"
• dic_runoff[Bool]=true, default_value=true, description="true to add additional DIC runoff terms to riverine (and atmosphere) fluxes so riverine DIC ~ TAlk, false to just use riverine DIC = 'carbw'"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
• SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_land_weathering_fluxes
  • fluxAtoLand_flux_CO2 –> fluxAtoLand.flux_CO2 (mol yr-1), VT_ReactContributor, description="flux CO2"
  • fluxAtoLand_flux_O2 –> fluxAtoLand.flux_O2 (mol yr-1), VT_ReactContributor, description="flux O2"
  • fluxRtoOcean_flux_DIC –> fluxRtoOcean.flux_DIC (mol yr-1), VT_ReactContributor, description="flux DIC"
  • fluxRtoOcean_flux_TAlk –> fluxRtoOcean.flux_TAlk (mol yr-1), VT_ReactContributor, description="flux TAlk"
  • fluxRtoOcean_flux_Ca –> fluxRtoOcean.flux_Ca (mol yr-1), VT_ReactContributor, description="flux Ca"
  • fluxRtoOcean_flux_P –> fluxRtoOcean.flux_P (mol yr-1), VT_ReactContributor, description="flux P"
  • fluxRtoOcean_flux_SO4 –> fluxRtoOcean.flux_SO4 (mol yr-1), VT_ReactContributor, description="flux SO4"
  • fluxLandtoSedCrust_flux_Ccarb –> fluxLandtoSedCrust.flux_Ccarb (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • fluxLandtoSedCrust_flux_Corg –> fluxLandtoSedCrust.flux_Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
  • fluxLandtoSedCrust_flux_GYP –> fluxLandtoSedCrust.flux_GYP (mol yr-1), VT_ReactContributor, description="flux GYP"
  • fluxLandtoSedCrust_flux_PYR –> fluxLandtoSedCrust.flux_PYR (mol yr-1), VT_ReactContributor, description="flux PYR"
  • tforce –> global.tforce (yr), VT_ReactDependency, description="time for external forcings"
  • UPLIFT –> global.UPLIFT (), VT_ReactDependency, description="uplift scaling"
  • PG –> global.PG (), VT_ReactDependency, description="paleogeographic forcing"
  • RHOSIL –> global.RHOSIL (), VT_ReactDependency, description="silicate weathering enhancement"
  • RHO –> global.RHO (), VT_ReactDependency, description="carbonate weathering enhancement"
  • F_EPSILON –> global.F_EPSILON (), VT_ReactDependency, description="phosphorus weathering enhancement"
  • CPland_relative –> global.CPland_relative (), VT_ReactDependency, description="land CP burial ratio scaling"
  • [COAL] –> global.COAL (), VT_ReactDependency, description="coal forcing"
  • GRAN_AREA (), VT_ReactDependency, description="granite area"
  • BA_AREA (), VT_ReactDependency, description="basalt area"
  • CARB_AREA (), VT_ReactDependency, description="carbonate area"
  • [ORG_AREA] (), VT_ReactDependency, description="organic carbon area"
  • [D_P_CO2_locb] (per mil), VT_ReactDependency, description="d13C fractionation between terrestrial organic burial and atmospheric CO2"
  • [D_eqbw_CO2] (per mil), VT_ReactDependency, description="d13C fractionation between atmospheric CO2 and fresh water"
  • [CO2_delta] –> atm.CO2_delta (per mil), VT_ReactDependency, description="atmospheric pCO2 delta 13C"
  • VEG (), VT_ReactDependency, description="Mass of terrestrial biosphere"
  • f_gran (), VT_ReactDependency, description="granite weathering rate"
  • f_bas (), VT_ReactDependency, description="basalt weathering rate"
  • f_ap (), VT_ReactDependency, description="apatite weathering rate"
  • f_carb (), VT_ReactDependency, description="carbonate weathering rate"
  • oxw_facO (), VT_ReactDependency, description="oxidative weathering oxygen dependence factor"
  • oxw_facOmax (), VT_ReactDependency, description="maximum possible oxidative weathering factor at high pO2"
  • C_norm –> sedcrust.C_norm (), VT_ReactDependency, description="Sedimentary carbonate normalized to present day"
  • [C_delta] –> sedcrust.C_delta (per mil), VT_ReactDependency, description="Sedimentary carbonate d13C"
  • G_norm –> sedcrust.G_norm (), VT_ReactDependency, description="Sedimentary organic carbon normalized to present day"
  • [G_delta] –> sedcrust.G_delta (per mil), VT_ReactDependency, description="Sedimentary organic carbon d13C"
  • [GYP_norm] –> sedcrust.GYP_norm (), VT_ReactDependency, description="Sedimentary gypsum normalized to present day"
  • [GYP_delta] –> sedcrust.GYP_delta (per mil), VT_ReactDependency, description="Sedimentary gypsum d34S"
  • [PYR_norm] –> sedcrust.PYR_norm (), VT_ReactDependency, description="Sedimentary pyrite normalized to present day"
  • [PYR_delta] –> sedcrust.PYR_delta (per mil), VT_ReactDependency, description="Sedimentary pyrite d34S"
  • granw_relative (), VT_ReactProperty, description="granite weathering normalized to present"
  • granw (molC/yr), VT_ReactProperty, description="granite weathering"
  • basw_relative (), VT_ReactProperty, description="basalt weathering normalized to present"
  • basw (molC/yr), VT_ReactProperty, description="basalt weathering"
  • silw (molC/yr), VT_ReactProperty, description="total silicate weathering"
  • silw_relative (), VT_ReactProperty, description="total silicate weathering normalized to present"
  • carbw_relative (), VT_ReactProperty, description="Carbonate weathering normalized to present"
  • carbw_fac (), VT_ReactProperty, description="Carbonate weathering normalized to present, without C reservoir dependence"
  • carbw (molC/yr), VT_ReactProperty, description="Carbonate weathering"
  • silwcarbw_relative (), VT_ReactProperty, description="total silicate and carbonate weathering, normalized to present"
  • orgcw (molC/yr), VT_ReactProperty, description="organic C erosion"
  • oxidw (molC/yr), VT_ReactProperty, description="Oxidative organic C weathering"
  • gypw (molS/yr), VT_ReactProperty, description="Gypsum weathering"
  • pyrw (molS/yr), VT_ReactProperty, description="Pyrite weathering"
  • granw_ap (molC/yr), VT_ReactProperty, description="apatite effective granite weathering flux"
  • basw_ap (molC/yr), VT_ReactProperty, description="apatite effective basalt weathering flux"
  • silw_ap (molC/yr), VT_ReactProperty, description="apatite effective total silicate weathering flux"
  • sedw_relative (), VT_ReactProperty, description="Other sediment weathering (sandstones etc) normalized to present"
  • phosw_x (molP/yr), VT_ReactProperty, description="Phosphorus weathering, other sediment associated"
  • phosw_s (molP/yr), VT_ReactProperty, description="Phosphorus weathering, silicate-associated"
  • phosw_c (molP/yr), VT_ReactProperty, description="Phosphorus weathering, carbonate-associated"
  • phosw_o (molP/yr), VT_ReactProperty, description="Phosphorus weathering, organic carbon-associated"
  • phosw (molP/yr), VT_ReactProperty, description="Phosphorus weathering, total"
  • pland (molP/yr), VT_ReactProperty, description="Phosphorus weathering to land"
  • psea (molP/yr), VT_ReactProperty, description="Phosphorus weathering to sea"
  • locb (molC/yr), VT_ReactProperty, description="Land organic carbon burial"
  • locb_delta (per mil), VT_ReactProperty, description="Land organic carbon burial d13C"

ReactionMarineBiotaCOPSE

COPSE Bergman(2004), COPSE Reloaded Lenton etal (2018) 0D marine biota

Parameters

• k1_oxfrac[Float64]=0.86, default_value=0.86, description="initial oxic fraction"
• k3_nfix[Float64]=8.75e12 (mol/yr), default_value=8.75e12, description="nitrogen fixation"
• k4_denit[Float64]=4.3e12 (mol/yr), default_value=4.3e12, description="denitrification"
• f_ncycle[Bool]=true, default_value=true, description="enable nitrogen cycle"
• f_nfix_power[Float64]=2.0, default_value=2.0, description="nitrogen fixation power-law dependence on nitrogen deficit wrt Redfield"
• f_nfix_nreplete[String]="Off", default_value="Off", allowed_values=["Off", "Sign"], description="nitrogen fixation when nitrogen excess wrt Redfield (only for bug compatitibility with COPSE 5_14 C code, which has Sign)"
• f_denit[String]="original", default_value="original", allowed_values=["original", "new"], description="functional form for denitrification"
• newp0[Float64]=225.956, default_value=225.956, description=""
• f_anoxia[String]="original", default_value="original", allowed_values=["original", "newanoxia"], description="functional form for marine anoxia function"
• k_logistic[Float64]=12.0, default_value=12.0, description="slope of logistic anoxia function"
• k_uptake[Float64]=0.5, default_value=0.5, description="efficiency of nutrient uptake in anoxia function"

Methods and Variables for default Parameters

• do_marinebiota
  • P (mol), VT_ReactDependency, description="Marine phosphorus"
  • N (mol), VT_ReactDependency, description="Marine nitrogen"
  • P_sms (mol yr-1), VT_ReactContributor, description="Marine phosphorus source-sinks"
  • N_sms (mol yr-1), VT_ReactContributor, description="Marine nitrogen source-sinks"
  • P_norm (), VT_ReactDependency, description="normalized Marine phosphorus"
  • N_norm (), VT_ReactDependency, description="normalized Marine nitrogen"
  • tforce –> global.tforce (yr), VT_ReactDependency, description="epoch for model forcing"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric pO2 normalized to present day"
  • Pconc (molP/kgsw), VT_ReactProperty, description="marine P conc"
  • newp (), VT_ReactProperty, description="marine new production"
  • newp_relative (), VT_ReactProperty, description="marine new production relative to present day"
  • ANOX (), VT_ReactProperty, description="marine anoxic fraction"
  • OX_relative (), VT_ReactProperty, description="marine oxic fraction relative to present day fraction 'k1_oxfrac'"
  • Nconc (molN/kgsw), VT_ReactProperty, description="marine N conc"
  • nfix (molN/yr), VT_ReactProperty, description="marine nitrogen fixation"
  • denit (molN/yr), VT_ReactProperty, description="marine denitrification"

ReactionOceanBurialCOPSE

COPSE Bergman(2004), COPSE Reloaded Lenton etal (2018) 0D ocean N, P, Corg, S burial

Fluxes are added to flux couplers:

• fluxOceanBurial: ocean burial fluxes

Parameters

• k2_mocb[Float64]=4.5e12 (mol/yr), default_value=4.5e12, description="ocean organic carbon burial"
• k6_fepb[Float64]=6.0e9 (mol/yr), default_value=6.0e9, description="Fe-P burial"
• k7_capb[Float64]=1.5e10 (mol/yr), default_value=1.5e10, description="Ca-P burial"
• enableS[Bool]=true, default_value=true, description="enable S burial"
• k_mpsb[Float64]=5.3e11 (mol S/yr), default_value=5.3e11, description="pyrite burial"
• k_mgsb[Float64]=1.0e12 (mol S/yr), default_value=1.0e12, description="gypsum burial"
• f_ncycle[Bool]=true, default_value=true, description="enable nitrogen cycle"
• f_CPsea[String]="Fixed", default_value="Fixed", allowed_values=["Fixed", "VCI"], description="Functional form of CPsea ratio"
• CPsea0[Float64]=250.0, default_value=250.0, description="for f_CPsea:"Fixed""
• f_CPsea_VCI_oxic[Float64]=217.0, default_value=217.0, description="Van Cappellen & Ingall (f_CPsea:"VCI") marine C/P burial ratio consts"
• f_CPsea_VCI_anoxic[Float64]=4340.0, default_value=4340.0, description="Van Cappellen & Ingall (f_CPsea:"VCI") marine C/P burial ratio consts"
• f_capb[String]="original", default_value="original", allowed_values=["original", "redox"], description="functional form of marine carbonate-associated P burial"
• f_fepb[String]="original", default_value="original", allowed_values=["original", "Dforced", "sfw", "pdep"], description="functional form of marine iron-associated P burial"
• CNsea0[Float64]=37.5, default_value=37.5, description="Always fixed"
• f_mocb[String]="original", default_value="original", allowed_values=["original", "Uforced", "O2dep", "both"], description="functinal form of marine organic carbon burial"
• f_mocb_b[Float64]=2.0, default_value=2.0, description="marine organic carbon burial power-law dependency on new production"
• f_pyrburial[String]="copse_O2", default_value="copse_O2", allowed_values=["copseO2", "copsenoO2"], description="Marine pyrite sulphur burial dependency on oxygen"
• SRedoxAlk[Bool]=false, default_value=false, description="true to include +TAlk from pyrite burial"
• f_sisotopefrac[String]="fixed", default_value="fixed", allowed_values=["fixed", "copse_O2"], description="S isotope fractionation calculation."
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
• SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_react
  • [fluxOceanBurial_flux_Corg] –> fluxOceanBurial.flux_Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
  • [fluxOceanBurial_flux_Porg] –> fluxOceanBurial.flux_Porg (mol yr-1), VT_ReactContributor, description="flux Porg"
  • [fluxOceanBurial_flux_Pauth] –> fluxOceanBurial.flux_Pauth (mol yr-1), VT_ReactContributor, description="flux Pauth"
  • [fluxOceanBurial_flux_PFe] –> fluxOceanBurial.flux_PFe (mol yr-1), VT_ReactContributor, description="flux PFe"
  • [fluxOceanBurial_flux_P] –> fluxOceanBurial.flux_P (mol yr-1), VT_ReactContributor, description="flux P"
  • [fluxOceanBurial_flux_GYP] –> fluxOceanBurial.flux_GYP (mol yr-1), VT_ReactContributor, description="flux GYP"
  • [fluxOceanBurial_flux_PYR] –> fluxOceanBurial.flux_PYR (mol yr-1), VT_ReactContributor, description="flux PYR"
  • O (mol), VT_ReactDependency, description="Atm-ocean oxygen (mol O2)"
  • P (mol), VT_ReactDependency, description="Marine phosphorus"
  • [DIC] (mol), VT_ReactDependency, description="ocean inorganic carbon"
  • [CAL] (mol), VT_ReactDependency, description="Marine calcium"
  • S (mol), VT_ReactDependency, description="Marine sulphate"
  • O_sms (mol yr-1), VT_ReactContributor, description="Atm-ocean oxygen (mol O2) source-sinks"
  • P_sms (mol yr-1), VT_ReactContributor, description="Marine phosphorus source-sinks"
  • [DIC_sms] (mol yr-1), VT_ReactContributor, description="ocean inorganic carbon source-sinks"
  • [CAL_sms] (mol yr-1), VT_ReactContributor, description="Marine calcium source-sinks"
  • S_sms (mol yr-1), VT_ReactContributor, description="Marine sulphate source-sinks"
  • N_sms (mol yr-1), VT_ReactContributor, description="Marine nitrogen source - sink"
  • O_norm (), VT_ReactDependency, description="normalized Atm-ocean oxygen (mol O2)"
  • P_norm (), VT_ReactDependency, description="normalized Marine phosphorus"
  • [DIC_norm] (), VT_ReactDependency, description="normalized ocean inorganic carbon"
  • [CAL_norm] (), VT_ReactDependency, description="normalized Marine calcium"
  • S_norm (), VT_ReactDependency, description="normalized Marine sulphate"
  • [D_mccb_DIC] (per mil), VT_ReactDependency, description="D13C marine calcite burial relative to ocean DIC"
  • [D_B_mccb_mocb] (per mil), VT_ReactDependency, description="D13C fractionation between marine organic and calcite burial"
  • [D_oceanDIC_A] (per mil), VT_ReactDependency, description="d13C fractionation between marine DIC and global DIC+CO2"
  • tforce –> global.tforce (yr), VT_ReactDependency, description="epoch for model forcing"
  • TEMP –> global.TEMP (K), VT_ReactDependency, description="global temperature"
  • [UPLIFT] –> global.UPLIFT (), VT_ReactDependency, description="UPLIFT forcing"
  • [DEGASS] –> global.DEGASS (), VT_ReactDependency, description="DEGASS forcing"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric pO2 normalized to present day"
  • [sfw_relative] –> oceanfloor.sfw_relative (), VT_ReactDependency, description="seafloor weathering relative to present"
  • newp_relative (), VT_ReactDependency, description="normalized marine new production"
  • ANOX (), VT_ReactDependency, description="marine anoxic fraction"
  • OX_relative (), VT_ReactDependency, description="marine oxic fraction relative to present day"
  • mocb_delta (per mil), VT_ReactProperty, description="D13C fractionation of marine organic carbon burial"
  • CPsea (), VT_ReactProperty, description="marine C:P ratio"
  • mocb (molC/yr), VT_ReactProperty, description="Marine organic carbon burial"
  • D_mpsb (per mil), VT_ReactProperty, description="D34S fractionation pyrite - marine sulphate"
  • monb (molN/yr), VT_ReactProperty, description="Marine organic N burial"

ReactionCarbBurialAlk

Marine carbonate burial from instantaneous alkalinity balance

Generates burial flux fluxOceanBurial.flux_Ccarb = 0.5 * flux_TAlk, adds reservoirs fluxes to DIC_sms and optionally CAL_sms.

Fluxes are added to flux couplers:

• fluxOceanBurial: ocean burial fluxes

Default linking for flux_TAlk is flux_TAlk -> fluxRtoOcean.flux_TAlk, ie carbonate burial sink for riverine alkalinity input.

Parameters

• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_carb_burial
  • flux_TAlk –> fluxRtoOcean.flux_TAlk (mol yr-1), VT_ReactDependency, description="riverine alkalinity flux"
  • mccb (molC/yr), VT_ReactProperty, description="Carbonate burial"
  • DIC_sms –> ocean.oceanfloor.DIC_sms (mol yr-1), VT_ReactContributor, description="DIC reservoir source - sink"
  • [CAL_sms] –> ocean.oceanfloor.CAL_sms (mol yr-1), VT_ReactContributor, description="Calcium reservoir source - sink"
  • flux_Ccarb –> fluxOceanBurial.flux_Ccarb (mol yr-1), VT_ReactContributor, description="carbonate burial"

ReactionSeafloorWeathering

COPSE Reloaded (Lenton etal 2018) seafloor weathering (basalt carbonation).

In a spatially resolved oceanfloor Domain, the total flux is calculated in the same way as for the 0D COPSE model, and is then distributed over a range of oceanfloor cells according the Paramter sfw_distribution_method.

Fluxes are added to flux couplers:

• fluxOceanfloor: ocean solute fluxes
• fluxOceanBurial: carbonate burial flux

Parameters

• f_sfw_opt[String]="sfw_temp", default_value="sfw_temp", allowed_values=["sfwtemp", "sfwstrong", "sfw_noT", "mills2014pCO2"], description="functional form for seafloor weathering rate temperature dependence"
• f_sfw_alpha[Float64]=0.23, default_value=0.23, description="power law for f_sfw_opt=mills2014pCO2 pCO2 dependence: wildly uncertain"
• f_sfw_force[String]="DEGASS", default_value="DEGASS", allowed_values=["None", "DEGASS"], description="seafloor weathering rate tectonic forcing"
• k_sfw[Float64]=3.0e12 (mol/yr), default_value=3.0e12, description="seafloor weathering rate"
• sfw_distribution_method[String]="Parameter", default_value="Parameter", allowed_values=["Parameter", "Depth"], description="method to set sfw distribution: Parameter - use sfw_distribution parameters, Depth - distribute proportional to area within specified depth range"
• sfw_distribution[Vector{Float64}]=[1.0], default_value=[1.0], description="per box distribution of seafloor weathering (length=Oceanfloor Domain size, must sum to 1.0)"
• sfw_depthrange[Vector{Float64}]=[-3000.0, -1000.0] (m), default_value=[-3000.0, -1000.0], description="depth range for distribution of seafloor weathering (lower, upper)"
• f_sfw_d13C[String]="delta_DIC", default_value="delta_DIC", allowed_values=["deltaDIC", "deltamccb"], description="d13C delta"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_seafloor_weathering
  • [fluxOceanBurial_flux_Ccarb] –> fluxOceanBurial.flux_Ccarb (mol yr-1), VT_ReactContributor, description="flux Ccarb"
  • [fluxOceanfloor_soluteflux_DIC] –> fluxOceanfloor.soluteflux_DIC (mol yr-1), VT_ReactContributor, description="flux DIC"
  • RHOSFW –> global.RHOSFW (), VT_ReactDependency, description="seafloor weathering-specific additional forcing (usually 1.0)"
  • [TEMP] –> global.TEMP (K), VT_ReactDependency, description="global mean temperature"
  • [DEGASS] –> global.DEGASS (), VT_ReactDependency, description="degass forcing"
  • [pCO2PAL] –> atm.pCO2PAL (), VT_ReactDependency, description="atmospheric pCO2PAL"
  • [DIC_delta] –> ocean.oceanfloor.DIC_delta (per mil), VT_ReactDependency, description="d13C DIC"
  • [D_mccb_DIC] –> ocean.D_mccb_DIC (per mil), VT_ReactDependency, description="d13C marine calcite burial relative to ocean DIC"
  • sfw_relative (), VT_ReactProperty, description="normalized seafloor weathering"
  • sfw (mol yr-1), VT_ReactProperty, description="seafloor weathering flux"
• totals
  • sfw (mol yr-1), VT_ReactDependency, description="seafloor weathering flux"
  • sfw_total (mol yr-1), VT_ReactProperty, description="total seafloor weathering flux"

ReactionSedCrustCOPSE

COPSE Bergman(2004), COPSE Reloaded Lenton etal (2018) metamorphic and volcanic "degassing" of sedimentary carbon and sulphur reservoirs.

Fluxes are added to flux couplers:

• fluxSedCrusttoAOcean: carbon and sulphur "degassing" fluxes

Parameters

• k12_ccdeg[Float64]=6.65e12 (mol/yr), default_value=6.65e12, description="carbonate C degassing rate"
• k13_ocdeg[Float64]=1.25e12 (mol/yr), default_value=1.25e12, description="org C degassing rate"
• enableS[Bool]=true, default_value=true, description="enable S degassing"
• k_pyrdeg[Float64]=0.0 (mol S/yr), default_value=0.0, description="pyrite degassing rate"
• k_gypdeg[Float64]=0.0 (mol S/yr), default_value=0.0, description="gypsum degassing rate"
• f_ocdeg[String]="O2indep", default_value="O2indep", allowed_values=["O2indep", "O2copsecrashprevent"], description="roll off orgC degassing at low pO2"
• CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
• SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

• do_sed_crust_COPSE
  • fluxSedCrusttoAOcean_flux_C –> fluxSedCrusttoAOcean.flux_C (mol yr-1), VT_ReactContributor, description="flux C"
  • fluxSedCrusttoAOcean_flux_Redox –> fluxSedCrusttoAOcean.flux_Redox (mol yr-1), VT_ReactContributor, description="flux Redox"
  • fluxSedCrusttoAOcean_flux_S –> fluxSedCrusttoAOcean.flux_S (mol yr-1), VT_ReactContributor, description="flux S"
  • C (mol), VT_ReactDependency, description="Sedimentary carbonate (mol C)"
  • G (mol), VT_ReactDependency, description="Sedimentary organic carbon (mol C)"
  • GYP (mol), VT_ReactDependency, description="Sedimentary gypsum (mol S)"
  • PYR (mol), VT_ReactDependency, description="Sedimentary pyrite (mol S)"
  • C_sms (mol yr-1), VT_ReactContributor, description="Sedimentary carbonate (mol C) source-sinks"
  • G_sms (mol yr-1), VT_ReactContributor, description="Sedimentary organic carbon (mol C) source-sinks"
  • GYP_sms (mol yr-1), VT_ReactContributor, description="Sedimentary gypsum (mol S) source-sinks"
  • PYR_sms (mol yr-1), VT_ReactContributor, description="Sedimentary pyrite (mol S) source-sinks"
  • C_norm (), VT_ReactDependency, description="normalized Sedimentary carbonate (mol C)"
  • G_norm (), VT_ReactDependency, description="normalized Sedimentary organic carbon (mol C)"
  • GYP_norm (), VT_ReactDependency, description="normalized Sedimentary gypsum (mol S)"
  • PYR_norm (), VT_ReactDependency, description="normalized Sedimentary pyrite (mol S)"
  • tforce –> global.tforce (yr), VT_ReactDependency, description="time for external forcings"
  • DEGASS –> global.DEGASS (), VT_ReactDependency, description="degassing scaling"
  • Bforcing –> global.Bforcing (), VT_ReactDependency, description="calcerous plankton evolution"
  • pO2PAL –> atm.pO2PAL (), VT_ReactDependency, description="atmospheric oxygen normalized to present-day"
  • ccdeg (molC/yr), VT_ReactProperty, description="Carbonate degassing"
  • ocdeg (molC/yr), VT_ReactProperty, description="Organic carbon degassing"
  • gypdeg (molS/yr), VT_ReactProperty, description="Gypsum degassing"
  • pyrdeg (molS/yr), VT_ReactProperty, description="Pyrite degassing"