-

genie-userconfigs/MS/stockeyetal.PNAS.2021/README.txt

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+################################################################
+### readme.txt #################################################
+################################################################
+
+For: 'Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology'
+
+Richard G. Stockey1*, Alexandre Pohl2,3, Andy Ridgwell2, Seth Finnegan4, and Erik A. Sperling1
+
+1 Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
+2 Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
+3 Biogéosciences, UMR 6282, UBFC/CNRS, Université Bourgogne Franche-Comté, 6 boulevard Gabriel, F-21000 Dijon, France
+4 Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
+* Corresponding author: rstockey@stanford.edu
+
+################################################################
+11/15/2020 -- README.txt file creation (R.G.S)
+################################################################
+
+Provided is the code used to create the model experiments presented in the paper.
+Also given are the configuration files necessary to run these experiments.
+
+The intention is to provide an opportunity to question the assumptions and
+interpretation through re-analysis and the creation of new and different experiments.
+(Plus, to provide a means to replicate results.)
+
+All experiments are run from: $HOME/cgenie.muffin/genie-main
+(unless a different installation directory has been used)
+
+All four O2-CO2 ensembles are described below using x-y placeholders for atmospheric O2 and CO2 
+concentrations as a function of preindustrial atmospheric levels (PAL)
+
+For each ensemble, all possible combinations of x and y are used, resulting in 42 simulations per ensemble
+O2 forcings (x) are the same across all ensembles
+CO2 forcings (y) are described separately for each ensemble
+
+x --> 0.05, 0.1, 0.2, 0.4, 0.6, 0.8, 1 [for all ensembles described below]
+
+######## model ensembles ##########################
+
+# Ordovician continental configuration
+y --> 4, 8, 16, 32, 64, 128
+./runmuffin.sh muffin.CB.fm0450dc.BASES MS/stockeyetal.PNAS.2021/fm0450.CO2.O2 muffin.CB.fm0450dc.BASES.yCO2.xO2.1EFD.config 10000
+
+# Permian continental configuration
+y --> 2, 4, 8, 16, 32, 64
+./runmuffin.sh cgenie.eb_go_gs_ac_bg.p0251b.BASES MS/stockeyetal.PNAS.2021/p0251.CO2.O2.ramp cgenie.eb_go_gs_ac_bg.p0251b.BASES.yCO2.xO2.1EFD.ramp.config 10000
+
+# Paleocene continental configuration
+y --> 0.5, 1, 2, 4, 8, 16
+./runmuffin.sh cgenie.eb_go_gs_ac_bg.p0055c.BASES MS/stockeyetal.PNAS.2021/p0055.CO2.O2.ramp cgenie.eb_go_gs_ac_bg.p0055c.BASES.yCO2.xO2.1EFD.ramp.config 20000
+
+# Ordovician continental configuration - shallow remineralization depth
+y --> 4, 8, 16, 32, 64, 128
+./runmuffin.sh muffin.CB.fm0450dc.BASES MS/stockeyetal.PNAS.2021/fm0450.CO2.O2.shallowremin muffin.CB.fm0450dc.BASES.yCO2.xO2.0.34EFD.config 10000
+
+################################################################
+################################################################
+################################################################

genie-userconfigs/MS/stockeyetal.PNAS.2021/fm0450.CO2.O2.shallow.remin/muffin.CB.fm0450dc.BASES.128CO2.0.05O2.0.34EFD.config

@@ -0,0 +1,70 @@
+#
+# --- CLIMATE --------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION --------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="bio_P"
+# [PO4] M-M half-sat value (mol kg-1)
+bg_par_bio_c0_PO4=0.10E-06
+# biological uptake time-scale
+bg_par_bio_tau=63.3827
+#
+# --- 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 -----------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=0.5
+# NO fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.0
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=200
+#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
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=15
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="pyyyyz.RpCO2_Rp13CO2.RpO2"
+bg_par_atm_force_scale_val_3=0.035584 # restoring forcing for pCO2 [atm]
+bg_par_atm_force_scale_val_6=0.010475 # restoring forcing for pO2 [atm]
+#
+# --- INITIAL CONDITIONS ---------------------------------------
+#
+# Ca
+bg_ocn_init_35=2.251E-02
+# Mg
+bg_ocn_init_50=2.392E-02
+# ALK
+bg_ocn_init_12=8.970E-02
+# DIC
+bg_ocn_init_3=9.091E-02
+#
+# --- END ------------------------------------------------------
+#
+#

genie-userconfigs/MS/stockeyetal.PNAS.2021/fm0450.CO2.O2.shallow.remin/muffin.CB.fm0450dc.BASES.128CO2.0.1O2.0.34EFD.config

@@ -0,0 +1,70 @@
+#
+# --- CLIMATE --------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION --------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="bio_P"
+# [PO4] M-M half-sat value (mol kg-1)
+bg_par_bio_c0_PO4=0.10E-06
+# biological uptake time-scale
+bg_par_bio_tau=63.3827
+#
+# --- 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 -----------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=0.5
+# NO fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.0
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=200
+#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
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=15
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="pyyyyz.RpCO2_Rp13CO2.RpO2"
+bg_par_atm_force_scale_val_3=0.035584 # restoring forcing for pCO2 [atm]
+bg_par_atm_force_scale_val_6=0.02095 # restoring forcing for pO2 [atm]
+#
+# --- INITIAL CONDITIONS ---------------------------------------
+#
+# Ca
+bg_ocn_init_35=2.251E-02
+# Mg
+bg_ocn_init_50=2.392E-02
+# ALK
+bg_ocn_init_12=8.970E-02
+# DIC
+bg_ocn_init_3=9.091E-02
+#
+# --- END ------------------------------------------------------
+#
+#

genie-userconfigs/MS/stockeyetal.PNAS.2021/fm0450.CO2.O2.shallow.remin/muffin.CB.fm0450dc.BASES.128CO2.0.2O2.0.34EFD.config

@@ -0,0 +1,70 @@
+#
+# --- CLIMATE --------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION --------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="bio_P"
+# [PO4] M-M half-sat value (mol kg-1)
+bg_par_bio_c0_PO4=0.10E-06
+# biological uptake time-scale
+bg_par_bio_tau=63.3827
+#
+# --- 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 -----------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=0.5
+# NO fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.0
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=200
+#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
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=15
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="pyyyyz.RpCO2_Rp13CO2.RpO2"
+bg_par_atm_force_scale_val_3=0.035584 # restoring forcing for pCO2 [atm]
+bg_par_atm_force_scale_val_6=0.0419 # restoring forcing for pO2 [atm]
+#
+# --- INITIAL CONDITIONS ---------------------------------------
+#
+# Ca
+bg_ocn_init_35=2.251E-02
+# Mg
+bg_ocn_init_50=2.392E-02
+# ALK
+bg_ocn_init_12=8.970E-02
+# DIC
+bg_ocn_init_3=9.091E-02
+#
+# --- END ------------------------------------------------------
+#
+#

genie-userconfigs/MS/stockeyetal.PNAS.2021/fm0450.CO2.O2.shallow.remin/muffin.CB.fm0450dc.BASES.128CO2.0.4O2.0.34EFD.config

@@ -0,0 +1,70 @@
+#
+# --- CLIMATE --------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION --------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="bio_P"
+# [PO4] M-M half-sat value (mol kg-1)
+bg_par_bio_c0_PO4=0.10E-06
+# biological uptake time-scale
+bg_par_bio_tau=63.3827
+#
+# --- 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 -----------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=0.5
+# NO fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.0
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=200
+#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
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=15
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="pyyyyz.RpCO2_Rp13CO2.RpO2"
+bg_par_atm_force_scale_val_3=0.035584 # restoring forcing for pCO2 [atm]
+bg_par_atm_force_scale_val_6=0.0838 # restoring forcing for pO2 [atm]
+#
+# --- INITIAL CONDITIONS ---------------------------------------
+#
+# Ca
+bg_ocn_init_35=2.251E-02
+# Mg
+bg_ocn_init_50=2.392E-02
+# ALK
+bg_ocn_init_12=8.970E-02
+# DIC
+bg_ocn_init_3=9.091E-02
+#
+# --- END ------------------------------------------------------
+#
+#