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genie-userconfigs/PUBS/published/vervoortetal.2024/README.txt
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| ################################################################ | ||
| ### README.txt ################################################# | ||
| ################################################################ | ||
|
|
||
| For: | ||
| 'Earth System Model Analysis of how Astronomical Forcing is Imprinted onto the Marine Geological Record: | ||
| The Role of the Inorganic (Carbonate) Carbon Cycle and Feedbacks' | ||
| P. Vervoort, S. Kirtland Turner, F. Rochholz, A. Ridgwell | ||
|
|
||
| ################################################################ | ||
| 06/15/2020 -- README.txt file creation (PV) | ||
| 07/01/2021 -- update (AR) | ||
| 07/23/2021 -- updated with new experiment names (PV) | ||
| 09/11/2023 -- add note (L.28); update experiment names | ||
| 14/02/2024 -- updated with reference directory (PV) | ||
| ################################################################ | ||
|
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| 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. | ||
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| 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.) | ||
|
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| All experiments are run from: | ||
| $HOME/cgenie.muffin/genie-main | ||
| (unless a different installation directory has been used) | ||
|
|
||
| ### NOTE ######################################################### | ||
| % 09/11/2023 - The manuscript has had some updates after publication | ||
| % in order to correct for an error in the insolation code. Commands | ||
| % below are used to run the updated simulations with corrected code | ||
| ################################################################# | ||
|
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| ### model experiments -- spinups ################################ | ||
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| The commands to run the spinups are listed as follows: | ||
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| fkl_pp30 => hemispherically symmetric continental configuration with one continent from pole-to-pole | ||
| fkl_np30 => hemispherically asymmetric continental configuration with one continent in the NH | ||
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| (1a) INITIAL SPINUP | ||
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| The initial, 1st-stage closed system spin-up needs 20 kyr to reach equilibrium: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_c.SPIN1 20000 | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_c.SPIN1 20000 | ||
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| (1b) Second Stage SPINUP | ||
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| The follow-on, 2nd-stage (accelerated) open system spin-up requires a long spinup time of 1.5 Myr to reach equilibrium | ||
|
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_c.SPIN2gl 1500000 fkl_pp30_c.SPIN1 | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_c.SPIN2gl 1500000 fkl_np30_c.SPIN1 | ||
|
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| ### model experiments -- main ensemble ########################## | ||
|
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| Below the commands to run the experiments with astronomical forcing for 4 Myr | ||
| Experiment 0-5 correspond to the numbering as described in the manuscript | ||
|
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| (2a) For EXPERIMENT 0, no carbon cycle feedbacks: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_EXP0_c.4Ma 4000000 fkl_pp30_c.SPIN2gl | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_EXP0_c.4Ma 4000000 fkl_np30_c.SPIN2gl | ||
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| (2b) For EXPERIMENT 1, climate + ocean circulation + CO2-ocean chemistry feedbacks only: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_EXP1_c.4Ma 4000000 fkl_pp30_c.SPIN2gl | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_EXP1_c.4Ma 4000000 fkl_np30_c.SPIN2gl | ||
|
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| (2c) For EXPERIMENT 2, EXPERIMENT 1 + primary productivity feedbacks: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_EXP2_c.4Ma 4000000 fkl_pp30_c.SPIN2gl | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_EXP2_c.4Ma 4000000 fkl_np30_c.SPIN2gl | ||
|
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| (2d) For EXPERIMENT 3, EXPERIMENT 2 + CaCO3 sedimentation feedbacks: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_EXP3_c.4Ma 4000000 fkl_pp30_c.SPIN2gl | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_EXP3_c.4Ma 4000000 fkl_np30_c.SPIN2gl | ||
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| (2e) For EXPERIMENT 4, EXPERIMENT 3 + weathering feedbacks: | ||
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| ./runmuffin.sh muffin.CBSG.fkl_pp30.BASES_PV PUBS/published/vervoortetal.2024 fkl_pp30_EXP4_c.4Ma 4000000 fkl_pp30_c.SPIN2gl | ||
| ./runmuffin.sh muffin.CBSG.fkl_np30.BASES_PV PUBS/published/vervoortetal.2024 fkl_np30_EXP4_c.4Ma 4000000 fkl_np30_c.SPIN2gl | ||
|
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||
| ################################################################ | ||
| ################################################################ | ||
| ################################################################ |
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genie-userconfigs/PUBS/published/vervoortetal.2024/fkl_np30_EXP0_c.4Ma
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| # | ||
| # | ||
| # --- CLIMATE --------------------------------------------------------- | ||
| # | ||
| # set NO CO2-climate feedback | ||
| ea_36=n | ||
| # set radiative forcing to 3x278ppm = 834 ppm (2.99x278 = 831 ppm) | ||
| ea_radfor_scl_co2=2.99 | ||
| # set seasonal cycle | ||
| ea_dosc=.true. | ||
| go_dosc=.true. | ||
| gs_dosc=.true. | ||
| # | ||
| # --- BIOLOGICAL NEW PRODUCTION --------------------------------------- | ||
| # | ||
| # FIX biological production in surface ocean w/ forcing file | ||
| bg_par_bio_prodopt="bio_POCflux" | ||
| # | ||
| # --- ORGANIC MATTER EXPORT RATIOS ------------------------------------ | ||
| # | ||
| # production fraction of dissolved organic matter | ||
| bg_par_bio_red_DOMfrac=0.66 | ||
| # | ||
| # --- INORGANIC MATTER EXPORT RATIOS ---------------------------------- | ||
| # | ||
| # fixed CaCO3:POC | ||
| bg_opt_bio_CaCO3toPOCrainratio='FIXED' | ||
| # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC) | ||
| bg_par_bio_red_POC_CaCO3=0.200 | ||
| # | ||
| # --- REMINERALIZATION ------------------------------------------------ | ||
| # | ||
| # 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 | ||
| # | ||
| # --- SEDIMENTS ---------------------------------------------------------- | ||
| # | ||
| # sediment grid options ==> defined in base-config | ||
| sg_par_sed_Dmax_neritic=500.0 | ||
| # sediment diagenesis options | ||
| sg_par_sed_diagen_CaCO3opt="ridgwell2001lookup" | ||
| sg_ctrl_sed_bioturb=.true. | ||
| sg_ctrl_sed_bioturb_Archer=.false. | ||
| sg_par_n_sed_mix=20 | ||
| # set invarient surface bioturbation mixing rate | ||
| sg_par_sed_mix_k_sur_max=0.15 | ||
| sg_par_sed_mix_k_sur_min=0.15 | ||
| # additional detrital flux (g cm-2 kyr-1) | ||
| sg_par_sed_fdet=0.180 | ||
| # | ||
| # --- WEATHERING ------------------------------------------------------ | ||
| # | ||
| # set a CLOSED system | ||
| bg_ctrl_force_sed_closedsystem=.true. | ||
| # set NO CaCO3 and CaSiO3 weathering-temperature feedback | ||
| rg_opt_weather_T_Ca=.false. | ||
| rg_opt_weather_T_Si=.false. | ||
| # weathering reference mean global land surface temperature (C) | ||
| rg_par_ref_T0=19.47 | ||
| #CO2 outgassing rate (mol C yr-1) | ||
| rg_par_outgas_CO2=6.1537e+12 | ||
| # global carbonate and silicate weathering rate (mol Ca2+ yr-1) | ||
| # derived from diag_weather_Ca.res of spin2 | ||
| rg_par_weather_CaSiO3=6.1537e+12 | ||
| rg_par_weather_CaCO3=6.1537e+12 | ||
| # d13C values | ||
| rg_par_outgas_CO2_d13C=-6.0 | ||
| rg_par_weather_CaCO3_d13C=13.77 | ||
| # | ||
| # --- DATA SAVING ----------------------------------------------------- | ||
| # | ||
| # date saving & reporting options | ||
| bg_par_data_save_level=8 | ||
| bg_ctrl_debug_lvl0=.true. | ||
| ma_debug_loop=1 | ||
| #(saves annual averages, NOT discrete values in time) | ||
| bg_par_infile_sig_name='save_timeseries_EVERY001000_orbits.dat' | ||
| bg_par_infile_slice_name='save_timeslice_EVERY002500_orbits.dat' | ||
| # representative NH latitude and season to sample orbital variation of insolation | ||
| bg_par_t_sig_count_N=12 | ||
| bg_par_sig_j_N=17 | ||
| # SH latitude/season | ||
| bg_par_t_sig_count_S=12 | ||
| bg_par_sig_j_S=2 | ||
| # | ||
| # --- FORCINGS -------------------------------------------------------- | ||
| # | ||
| # specify POC forcing field | ||
| bg_par_forcing_name="pyyyyz.FPOC_np30.vervoortetal2021" | ||
| # re-scale gas transfer coeff to give ~0.058 mol m-2 yr-1 uatm-1 global mean air-sea coefficient (original: 0.310) | ||
| bg_par_gastransfer_a=0.715813093980993 | ||
| # select correct insolation code | ||
| ea_opt_orbit_old=.false. | ||
| # Call orbit_radfor | ||
| ea_38="y" | ||
| # Specify the type of orbital forcing default (0), time-varying (1), alternative config (2) | ||
| ea_39=1 | ||
| # Number of data points in orbits file | ||
| ea_40=5000 | ||
| # Interval between data points in goldstein time steps | ||
| ea_41=48000 | ||
| # filename for orbital parameters (must be in genie-embm/data/input) | ||
| ea_42="orbits_La2004_57.93_52.91Ma_new.dat" | ||
| # | ||
| # --- MISC ----------------------------------------------------- | ||
| # | ||
| # add ventillation tracers | ||
| bg_ctrl_force_ocn_age1=.true. | ||
| # | ||
| # --- END ------------------------------------------------------ | ||
| # |
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genie-userconfigs/PUBS/published/vervoortetal.2024/fkl_np30_EXP1_c.4Ma
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| Original file line number | Diff line number | Diff line change |
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| # | ||
| # | ||
| # --- CLIMATE --------------------------------------------------------- | ||
| # | ||
| # set climate feedback | ||
| ea_36=y | ||
| # set seasonal cycle | ||
| ea_dosc=.true. | ||
| go_dosc=.true. | ||
| gs_dosc=.true. | ||
| # | ||
| # --- BIOLOGICAL NEW PRODUCTION --------------------------------------- | ||
| # | ||
| # FIX biological production in surface ocean w/ forcing file | ||
| bg_par_bio_prodopt="bio_POCflux" | ||
| # | ||
| # --- ORGANIC MATTER EXPORT RATIOS ------------------------------------ | ||
| # | ||
| # production fraction of dissolved organic matter | ||
| bg_par_bio_red_DOMfrac=0.66 | ||
| # | ||
| # --- INORGANIC MATTER EXPORT RATIOS ---------------------------------- | ||
| # | ||
| # fixed CaCO3:POC | ||
| bg_opt_bio_CaCO3toPOCrainratio='FIXED' | ||
| # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC) | ||
| bg_par_bio_red_POC_CaCO3=0.200 | ||
| # | ||
| # --- REMINERALIZATION ------------------------------------------------ | ||
| # | ||
| # 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 | ||
| # | ||
| # --- SEDIMENTS ---------------------------------------------------------- | ||
| # | ||
| # sediment grid options ==> defined in base-config | ||
| sg_par_sed_Dmax_neritic=500.0 | ||
| # sediment diagenesis options | ||
| sg_par_sed_diagen_CaCO3opt="ridgwell2001lookup" | ||
| sg_ctrl_sed_bioturb=.true. | ||
| sg_ctrl_sed_bioturb_Archer=.false. | ||
| sg_par_n_sed_mix=20 | ||
| # set invarient surface bioturbation mixing rate | ||
| sg_par_sed_mix_k_sur_max=0.15 | ||
| sg_par_sed_mix_k_sur_min=0.15 | ||
| # additional detrital flux (g cm-2 kyr-1) | ||
| sg_par_sed_fdet=0.180 | ||
| # | ||
| # ******* Corg burial ******* | ||
| # N/A | ||
| # | ||
| # --- WEATHERING ------------------------------------------------------ | ||
| # | ||
| # set a CLOSED system | ||
| bg_ctrl_force_sed_closedsystem=.true. | ||
| # set NO CaCO3 and CaSiO3 weathering-temperature feedback | ||
| rg_opt_weather_T_Ca=.false. | ||
| rg_opt_weather_T_Si=.false. | ||
| # weathering reference mean global land surface temperature (C) | ||
| rg_par_ref_T0=19.47 | ||
| #CO2 outgassing rate (mol C yr-1) | ||
| rg_par_outgas_CO2=6.1537e+12 | ||
| # global carbonate and silicate weathering rate (mol Ca2+ yr-1) | ||
| # derived from diag_weather_Ca.res of spin2 | ||
| rg_par_weather_CaSiO3=6.1537e+12 | ||
| rg_par_weather_CaCO3=6.1537e+12 | ||
| # d13C values | ||
| rg_par_outgas_CO2_d13C=-6.0 | ||
| rg_par_weather_CaCO3_d13C=13.77 | ||
| # | ||
| # --- DATA SAVING ----------------------------------------------------- | ||
| # | ||
| # date saving & reporting options | ||
| bg_par_data_save_level=8 | ||
| bg_ctrl_debug_lvl0=.true. | ||
| ma_debug_loop=1 | ||
| #(saves annual averages, NOT discrete values in time) | ||
| bg_par_infile_sig_name='save_timeseries_EVERY001000_orbits.dat' | ||
| bg_par_infile_slice_name='save_timeslice_EVERY002500_orbits.dat' | ||
| # representative NH latitude and season to sample orbital variation of insolation | ||
| bg_par_t_sig_count_N=12 | ||
| bg_par_sig_j_N=17 | ||
| # SH latitude/season | ||
| bg_par_t_sig_count_S=12 | ||
| bg_par_sig_j_S=2 | ||
| # | ||
| # --- FORCINGS -------------------------------------------------------- | ||
| # | ||
| # specify POC forcing field | ||
| bg_par_forcing_name="pyyyyz.FPOC_np30.vervoortetal2021" | ||
| # re-scale gas transfer coeff to give ~0.058 mol m-2 yr-1 uatm-1 global mean air-sea coefficient (original: 0.310) | ||
| bg_par_gastransfer_a=0.715813093980993 | ||
| # select correct insolation code | ||
| ea_opt_orbit_old=.false. | ||
| # Call orbit_radfor | ||
| ea_38="y" | ||
| # Specify the type of orbital forcing default (0), time-varying (1), alternative config (2) | ||
| ea_39=1 | ||
| # Number of data points in orbits file | ||
| ea_40=5000 | ||
| # Interval between data points in goldstein time steps | ||
| ea_41=48000 | ||
| # filename for orbital parameters (must be in genie-embm/data/input) | ||
| ea_42="orbits_La2004_57.93_52.91Ma_new.dat" | ||
| # | ||
| # --- MISC ----------------------------------------------------- | ||
| # | ||
| # add ventillation tracers | ||
| bg_ctrl_force_ocn_age1=.true. | ||
| # | ||
| # --- END ------------------------------------------------------ | ||
| # |
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