diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.000 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.000 deleted file mode 100644 index a6aac6d0d..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.000 +++ /dev/null @@ -1,126 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY ME! -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=3.9109 -# NOTE: for worjh2:: @ x1, mean SST (total surface) == 18.059197 -# @ x8, mean SST (total surface) == 25.446050 -# => 7.3869 C of warming for 3 doublings (x1 -> x8) -# => 2.46 C climate sensitivity -# Phanerozoic mean ~ 22.9 C -# => to achive 4.84 C of warming (compared to x1) requires 1.9675 doublings -# => x 3.9109 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.020 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.020 deleted file mode 100644 index 00291c174..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.020 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=6.4108 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.040 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.040 deleted file mode 100644 index 6af07dbd3..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.040 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=7.7291 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.060 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.060 deleted file mode 100644 index 9d00521db..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.060 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=7.4252 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.080 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.080 deleted file mode 100644 index aa810aae3..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.080 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=4.4561 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.100 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.100 deleted file mode 100644 index 7e81b8fa8..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.100 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.4601 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.120 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.120 deleted file mode 100644 index e7265e6fa..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.120 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=8.4424 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.140 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.140 deleted file mode 100644 index 7210a8087..000000000 Binary files a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.140 and /dev/null differ diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.160 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.160 deleted file mode 100644 index 0da5e1ea4..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.160 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=13.6673 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.180 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.180 deleted file mode 100644 index 94de15efc..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.180 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=24.3626 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.200 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.200 deleted file mode 100644 index 4ced68c4e..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.200 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=20.8309 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.220 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.220 deleted file mode 100644 index 290c79336..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.220 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=24.7191 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.240 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.240 deleted file mode 100644 index bddde72b4..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.240 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=27.8633 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.280 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.280 deleted file mode 100644 index 107b9333c..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.280 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.7831 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.300 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.300 deleted file mode 100644 index d49c442ea..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.300 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=6.4745 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.320 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.320 deleted file mode 100644 index dbb68ebfd..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.320 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=6.0317 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.340 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.340 deleted file mode 100644 index c59cdc198..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.340 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=4.955 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.360 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.360 deleted file mode 100644 index 701cf325a..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.360 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.6827 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.380 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.380 deleted file mode 100644 index 19f424e73..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.380 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=4.3986 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.400 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.400 deleted file mode 100644 index fa41998d3..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.400 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=3.6442 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.420 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.420 deleted file mode 100644 index eb8b10c73..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.420 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.0165 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.440 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.440 deleted file mode 100644 index 17bba6d1c..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.440 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.3245 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.460 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.460 deleted file mode 100644 index 8467b9510..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.460 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.7353 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.480 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.480 deleted file mode 100644 index 5ec51656e..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.480 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.6691 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.500 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.500 deleted file mode 100644 index 66dbd9a15..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.500 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.623 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.520 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.520 deleted file mode 100644 index 084b096f2..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.520 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.177 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.540 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.540 deleted file mode 100644 index 1616636ce..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.540 +++ /dev/null @@ -1,119 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY MATLAB -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=5.9996 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.635 b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.635 deleted file mode 100644 index 207443f87..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/muffin.CB.BASESCH4.xxRF.635 +++ /dev/null @@ -1,124 +0,0 @@ -# ******************************************************************* -# *** USERCONFIG.MODERN.BIOGEM.PO4.SPIN ***************************** -# ******************************************************************* -# -# *** CLIMATE ******************************************************* -# -# set NO climate feedback (climate NOT responding to changing pCH4) -ea_36=n -# -# *** ATMOSPHERIC PHOTOCHEMISTRY ************************************ -# -# atmospheric photochemical scheme ID string -ac_par_atm_CH4_photochem="claire06" -# -# *** BIOLOGICAL NEW PRODUCTION ************************************* -# -# *** optional changes to align with PALEO recommendations ********** -bg_par_bio_prodopt="bio_P" -bg_par_bio_tau=63.3827 -bg_par_bio_c0_PO4=0.10E-06 -# -# *** ORGANIC MATTER EXPORT RATIOS ********************************** -# -# production fraction of dissolved organic matter -bg_par_bio_red_DOMfrac=0.66 -# -# *** INORGANIC MATTER EXPORT RATIOS ******************************** -# -# SET NO PELAGIC CARBONATE PRODUCTION -bg_par_bio_red_POC_CaCO3=0.0 -bg_par_bio_red_POC_CaCO3_pP=0.0 -# -# *** REMINERALIZATION ********************************************** -# -# set remineralization scheme [e.g., hard thresholds 'true' // 'false'] -bg_ctrl_bio_remin_thresh=.false. -# half-saturation constant for oxic remin -bg_par_bio_remin_c0_O2=1.0E-07 -# inhibition constant for oxic remin -bg_par_bio_remin_ci_O2=1.0E-06 -# half-saturation constant for sulphate reduction -bg_par_bio_remin_c0_SO4=5.0E-04 -# inhibition constant for sulphate reduction -bg_par_bio_remin_ci_SO4=5.0E-04 -# DOC lifetime (yrs) -bg_par_bio_remin_DOMlifetime=0.5 -# initial fractional abundance of POC component #2 -bg_par_bio_remin_POC_frac2=0.0557 -# depth of remineralization or particulate organic matter -bg_par_bio_remin_POC_eL1=589.9451 -# remineralization length #2 for POC -bg_par_bio_remin_POC_eL2=1000000.0 -# initial fractional abundance of CaCO3 component #2 -bg_par_bio_remin_CaCO3_frac2=0.45 -# depth of remineralization or CaCO3 -bg_par_bio_remin_CaCO3_eL1=1.8905e+003 -# remineralization length #2 for CaCO3 -bg_par_bio_remin_CaCO3_eL2=1000000.0 -# sulfide oxidation rate form -bg_opt_bio_remin_oxidize_H2StoSO4="OLD" -# sulfide oxidation rate constant [only used if rate law is linear] -#bg_par_bio_remin_kH2StoSO4=1.0E07 -# rate constant for aerobic methanotrophy -bg_par_bio_remin_AER_kAER=0.10 -# O2 half-saturation constant for aerobic methanotrophy -bg_par_bio_remin_AER_Km_O2=20.E-06 -# rate constant for AOM -bg_par_bio_remin_AOM_kAOM=0.01 -# SO4 half-saturation constant for AOM -bg_par_bio_remin_AOM_Km_SO4=500.0E-06 -# enable/disable thermodynamic terms -bg_par_bio_remin_AER_thermo="on" -bg_par_bio_remin_AOM_thermo="on" -# biological energy quanta (BEQ) for CH4 oxidation -bg_par_bio_remin_AER_BEQ=15.0 -bg_par_bio_remin_AOM_BEQ=15.0 -# methanogenesis 13C fractionation -bg_par_d13C_Corg_CH4_epsilon=-35.0 -# -# *** DATA SAVING *************************************************** -# -# BASIC + biology + FULL (inc. redox) geochem diagnostics -bg_par_data_save_level=15 -# force time-slice save at run end only -bg_par_infile_slice_name='save_timeslice_NONE.dat' -# -# *** FORCINGS ****************************************************** -# -# -# *** MISC ********************************************************** -# -# *** optional changes to align with PALEO recommendations ********** -# set 'instantaneous' water column remineralziation -bg_par_bio_remin_sinkingrate_physical=9.9E9 -bg_par_bio_remin_sinkingrate_reaction=125.0 -# maximum time-scale to geochemical reaction completion (days) -bg_par_bio_geochem_tau=45.0 -# extend solubility and geochem constant T range (leave S range as default) -gm_par_geochem_Tmin = -2.0 -gm_par_geochem_Tmax = 45.0 -gm_par_carbchem_Tmin = -2.0 -gm_par_carbchem_Tmax = 45.0 -# -# *** INITIAL CONDITIONS ******************************************** -# -# set initial carbonate chemsitry state -ac_atm_init_3=2224.0E-06 # pCO2 -- 'carbon dioxide (CO2)' -ac_atm_init_4=0.0 # pCO2_13C -- 'd13C CO2' -bg_ocn_init_3=5259.186E-6 # DIC -- 'dissolved inorganic carbon (DIC)' -bg_ocn_init_4=0.0 # DIC_13C -- 'd13C of DIC' -bg_ocn_init_12=5227.416E-6 # ALK -- 'alkalinity (ALK)' -# -# ******************************************************************* -# *** END *********************************************************** -# ******************************************************************* -# -# >>> ADDED BY ME! -# scaling for atmospheric CO2 radiative forcing, relative to 278 ppm -ea_radfor_scl_co2=57.2737 -# NOTE: for fm0635ca:: @ x8, mean SST (total surface) == 15.913961 -# from worjh2: climate sensitivity == 2.46 C -# Phanerozoic mean ~ 22.9 C -# => to achive 6.9860 C of warming (compared to x8) requires a further 2.8398 doublings -# => 8*2^2.8398 = x 57.2737 diff --git a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/readme.txt b/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/readme.txt deleted file mode 100644 index 7d8b3d8ed..000000000 --- a/genie-userconfigs/PUBS/submitted/Marshall_et_al.2024/readme.txt +++ /dev/null @@ -1,119 +0,0 @@ -================================================================ -=== readme.txt ================================================= -================================================================ - -Provided are as part of the code release the configuration files necessary to run the key model experiments presented in the paper. -The intention is to provide an oppertunity to question the paper assumptions and interpretation through re-analysis, -as well as the creation of new and different experiments. (Plus, to provide a means to replicate published results.) -This readme file details how the experiments can be run. -Refer to the mufifn manual: -https://github.com/derpycode/muffindoc -for details on model code installation and configuration, locating and visualizing model results, etc. - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -PUBLICATION DETAILS [summary of manuscript/publication] -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -Extreme ocean methane cycling during the early Phanerozoic -Nathan Marshall1, Megan Rohrssen1,2, Andy Ridgwell1, Alexandre Pohl3, Bradley D. Cramer4, Woodward W. Fischer5, Olle Hints6, Chris Holmden7, Pavel Kabanov8, Alison Kuhl9, Carina Lee1,10, Michael J. Melchin11, Christopher T. Reinhard12, Richard D. Pancost13, Gordon D . Love1 -1Department of Earth Sciences, University of California, Riverside, CA, 92521, USA. -2Department of Earth and Atmospheric Sciences, Central Michigan University, Mt. Pleasant, MI 48859, USA. -3Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France. -4Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA. -5Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA. -6Institute of Geology at Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia. -7Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada. -8Geological Survey of Canada Calgary, Calgary, AB T2L 2A7, Canada. -9School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK. -10Lunar & Planetary Institute, Universities Space Research Association, Houston, TX 77058, USA. -11Department of Earth Sciences, St. Francis Xavier University, Antigonish, NS, Canada B2G 2W5. -12School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA. -13School of Chemistry, School of Earth Sciences, Cabot Institute for the Environment, University of Bristol, BS8 1TS Bristol, UK. - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -EDITING LOG [list of changes made to this file, when, and by who] -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -2023/12/05 -- README.txt file created by [AR] - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -IMPORTANT! -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -In this initial release, all the files are on a development branch. - -To aceess and run -- from cgenie.muffin, type: - -git checkout _DEV_FeNIP2_masterupdated - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -SUMMARY OF EXPERIMENTS [summerize experiments detailed and in which e.g. figures they appear] -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -As per (loosly paraphrasing) Methods: - -The model is configured with 28 different sets of boundary conditions (continental distribution and ocean bathymetry, wind velocity and stress, planetary albedo, and greenhouse gas forcing). For 20 through 540 Ma (at 20 Myr intervals) these boundary conditions follow Pohl et al. [2022]. Our 0 Ma (present-day) configuration follows Cao et al. [2009] while 635 Ma (Cryogenian) follows Reinhard et al. [2020] , with the exception that we adjust (via pCO2) the annual mean global ocean surface temperature to match that of the 20 through 540 Ma time-slices (Pohl et al. [2022]). The representation of ocean-atmosphere biogeochemical cycling (of carbon (and isotopes), alkalinity, phosphate, oxygen, sulphur (SO4 and H2S), and CH4 (and isotopes)) follows Reinhard et al. [2020]. For each of the total 28 continental configurations we varied the assumed value of atmospheric pO2 and ocean SO4 concentration in the range ×0.2, ×0.5, and ×1.0 the respective modern (0.21 atm for pO2, and 28 mmol kg-1 for [SO4]) in all 9 permutations. Each modern ensemble member (9 redox permutations of each of 28 different time-slices) was run for 10,000 years, and we report the annual average from the last year of each simulation. In a second series of ensembles, rather than adopt the default vertical depth scale of remineralization of particulate organic matter (590 m (Cao et al. [2009])), we halved it (295 m) to represent a potential earlier Earth, ocean biogeochemical state characterized by shallower recycling of nutrients and carbon and the Mesozoic advent of planktic biomineralization (and increasingly complex ecosystem processing of primary production) (Meyer et al. [2016 ]; Lu et al. [2018 ]). - -All the base-config and boundary configuration files required are included as part of the code release. - -*** ensemble series #1 *** - -User-configuration files are provided (this directory) for all 28 different time-slices, but all for modern pO2 and ocean SO4, and for the default POM reminerilization depth (590 m). - -To change any one time-slice to represent a different ensemble member -- at the end of the user-config file, edit the parameters lines: - -# atmospheric pO2 (atm) -- modern default = 0.21 -ac_atm_init_6=0.210 -# ocean SO4 (mol kg-1) -- modern default = 0.28 -bg_ocn_init_38=0.028 - -The published ensemble members multiple these values by 0.2, 0.5, or 1.0, in all (9) permutations. - -The results of these experiments are shown in Figure 2. - -*** ensemble series #2 *** - -To generate the 2nd series of time-slices and redox parameter ensembles, simply add the following line at the end: - -# depth of remineralization of particulate organic matter (m) -bg_par_bio_remin_POC_eL1=294.9726 - -(which over-rides a setting earlier in the file) - -Note that only a small sub-set fo the entire ensemble series #2 is shown in Figure 2. - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -RUNNING THE EXPERIMENTS [command lines, broken down in sub-sections for spinups, main experiments, SI, etc where appropriate] -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -To run any of the 20 Ma through 540 Ma experiments: - -./runmuffin.sh muffin.CB.???rdP1_.BASESCH4 PUBS/submitted/Marshall_et_al.2024 muffin.CB.BASESCH4.xxRF.??? 10000 - -where ??? is the code for the time-slice and is one of: - -000 -020 -040 -... -500 -520 -540 - -For modern (O Ma), the command is: - -./runmuffin.sh muffin.CB.p_worjh2.BASESCH4 PUBS/submitted/Marshall_et_al.2024 muffin.CB.BASESCH4.xxRF.000 10000 - -and for 635 Ma: - -./runmuffin.sh muffin.CB.fm0635ca.BASESCH4 PUBS/submitted/Marshall_et_al.2024 muffin.CB.BASESCH4.xxRF.635 10000 - -++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ - -Note that all experiments are run from: -$HOME/cgenie.muffin/genie-main -(unless a different installation directory has been used) - -================================================================ -================================================================ -================================================================ \ No newline at end of file