Merge pull request #115 from FormingWorlds/dummy_escape

Dummy escape module

docs/source/usage.rst

@@ -18,10 +18,11 @@ You can also run PROTEUS inside a Screen session using:
 
    .. code-block:: console
 
-         $  tools/RunPROTEUS.sh [cfgfile] [alias] [detach]
+         $  tools/RunPROTEUS.sh [cfgfile] [alias] [resume] [detach]
    
 Which runs PROTEUS using the config file ``[cfgfile]`` inside a Screen session with the 
-name ``[alias]``. The ``[detach]`` parameter (y/n) tells the session whether to immediately 
+name ``[alias]``. The ``[resume]`` parameter (y/n) tells the model whether to resume from 
+a previous state. The ``[detach]`` parameter (y/n) tells the session whether to immediately 
 detach or not. This allows multiple instances of the model to be dispatched easily and 
 safely.
 
@@ -239,7 +240,7 @@ configuration, but they must all be passed via the config file.
      - Greater than zero.  
 
    * - ``shallow_ocean_layer``
-     - Legaacy method for converging atmospheric and interior upward fluxes. 
+     - Legacy method for converging atmospheric and interior upward fluxes. 
      - True
      - Integer
      - 0: Off, 1: On
@@ -256,6 +257,24 @@ configuration, but they must all be passed via the config file.
      - Float
      - Greater than or equal to 0. Set to 0 to disable.    
 
+  * - ``escape_model``
+     - Escape model to be used.
+     - False
+     - Integer
+     - 0: None, 1: ZEPHYRUS, 2: Dummy 
+
+  * - ``escape_stop``
+     - Stop the simulation when the atmosphere mass drops below this fraction of its initial mass.
+     - False
+     - Float
+     - Values between zero and unity (exclusive).
+
+  * - ``escape_dummy_rate``
+     - Bulk escape rate for dummy escape model [kg s-1]
+     - False
+     - Float
+     - Any reasonable positive value.
+
    * - ``prevent_warming``
      - Flag to ensure that the net upward energy flux is always positive, which prevents the star from causing net heating inside the planet.   
      - False

examples/dummy_atmosphere/init_coupler.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e2    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled

examples/earth_demo/init_coupler.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e4    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled

input/default.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e4    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
@@ -75,6 +74,11 @@ steady_dprel                = 1.0e-9   # Percentage change in melt fraction over
 emit_stop                   = 1         # Enable this break condition
 F_crit                      = 0.2       # Critical flux, below which the model will terminate
 
+# Atmospheric escape 
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
 # Method for solving for T(p) profile
 atmosphere_model            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI
 atmosphere_solve_energy     = 0         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 

input/dummy.cfg

@@ -45,38 +45,42 @@ stellar_heating             = 1
 plot_iterfreq               = 1      # Plotting frequency, 0: wait until completion | n: every n iterations
 plot_format                 = png  # Plotting image file format
 sspec_dt_update             = 1e9    # Time intervals at which to re-calculate the stellar spectrum
-sinst_dt_update             = 1e2    # Time intervals at which to re-calculate the instellation
+sinst_dt_update             = 1e1    # Time intervals at which to re-calculate the instellation
 dt_maximum                  = 3e7    # Maximum time-step
 dt_minimum                  = 1e2    # Minimum time-step
 dt_method                   = 1      # Time-stepping method, 0: proportional | 1: adaptive | 2: maximum
 dt_propconst                = 52.0   # Proportionality constant for dt_method=0
-dt_atol                     = 0.02  # Step size atol
-dt_rtol                     = 0.07   # Step size rtol
+dt_atol                     = 0.02   # Step size atol
+dt_rtol                     = 0.10   # Step size rtol
 dt_initial                  = 1e2    # Inital step size
 
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
 
 # Break at solidification?
-solid_stop                  = 1
+solid_stop                  = 0
 phi_crit                    = 0.005     # melt fraction
 
 # Break at steady state?
-steady_stop                 = 1
+steady_stop                 = 0
 steady_flux                 = 0.8        # Maximum absolute value of F_atm allowed for convergence
 steady_dprel                = 1.0e-9     # Percentage change in melt fraction over time (dp/p)/dt*100
 
 # Break at small flux?
-emit_stop                   = 1         # Enable this break condition
+emit_stop                   = 0         # Enable this break condition
 F_crit                      = 0.2       # Model will terminate when |F_atm| < F_crit
 
+# Atmospheric escape 
+escape_model                = 2         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 2e7       # Bulk escape rate for dummy escape model [kg s-1]
+
 # Method for solving for T(p) profile
-atmosphere_model            = 2         # Atmosphere model to be used, 0: JANUS | 1: AGNI
+atmosphere_model            = 2         # Atmosphere model to be used, 0: JANUS | 1: AGNI | 2: Dummy
 atmosphere_solve_energy     = 0         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 
 atmosphere_surf_state       = 1        # Atmosphere bottom edge boundary condition, 0: free | 1: fixed at T_surf | 2: conductive skin
 
@@ -115,10 +119,10 @@ mixing_length               = 2
 solver_tolerance            = 1.0e-10
 
 # Maximum absolute surface temperature change [K]
-tsurf_poststep_change       = 20.0  
+tsurf_poststep_change       = 30.0  
 
 # Maximum fractional surface temperature change [fraction]
-tsurf_poststep_change_frac  = 0.01
+tsurf_poststep_change_frac  = 0.02
 
 # Fractional core radius
 planet_coresize             = 0.55
@@ -131,13 +135,13 @@ ic_dsdr                     = -4.698e-06
 F_atm                       = 1e6
 
 # Oxygen fugacity offset relative to the IW buffer (log10 units)
-fO2_shift_IW                = 4
+fO2_shift_IW                = 2
 
 # Enable solving for initial partial pressures (0: off | 1: on)
-solvevol_use_params          = 0
+solvevol_use_params          = 1
 
 # Parameters used to solve for initial partial pressures (when solvepp_use_params = 1)
-T_magma                     = 1900      # Surface temperature initial guess [K]
+T_magma                     = 3000      # Surface temperature initial guess [K]
 Phi_global                  = 1.0       # Mantle melt fraction initial guess
 CH_ratio                    = 1.0       # C/H ratio
 hydrogen_earth_oceans       = 6.0       # Hydrogen inventory in units of equivalent Earth oceans
@@ -147,7 +151,7 @@ sulfur_ppmw                 = 200.0     # Sulfur inventory in ppmw relative to m
 # Prescribed injected partial pressures [bar]
 # Summed with solvepp results when solvepp_enabled = 1
 H2O_included                = 1
-H2O_initial_bar             = 30.0
+H2O_initial_bar             = 0.0
 
 CO2_included                = 1
 CO2_initial_bar             = 0.0
@@ -158,15 +162,15 @@ N2_initial_bar              = 0.0
 S2_included                 = 1
 S2_initial_bar              = 0.0
 
-SO2_included                = 0
+SO2_included                = 1
 SO2_initial_bar             = 0.0
 
-H2_included                 = 0
+H2_included                 = 1
 H2_initial_bar              = 0.0
 
-CH4_included                = 0
+CH4_included                = 1
 CH4_initial_bar             = 0.0
 
-CO_included                 = 0
+CO_included                 = 1
 CO_initial_bar              = 0.0
 

input/janus_mixed.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e4    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
@@ -75,6 +74,11 @@ steady_dprel                = 1.0e-9     # Percentage change in melt fraction ov
 emit_stop                   = 1         # Enable this break condition
 F_crit                      = 0.2       # Model will terminate when |F_atm| < F_crit
 
+# Atmospheric escape 
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
 # Method for solving for T(p) profile
 atmosphere_model            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI
 atmosphere_solve_energy     = 0         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 

input/jgr_grid.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 8e2    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
@@ -75,6 +74,11 @@ steady_dprel                = 1.0e-9     # Percentage change in melt fraction ov
 emit_stop                   = 1         # Enable this break condition
 F_crit                      = 0.2       # Model will terminate when |F_atm| < F_crit
 
+# Atmospheric escape 
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
 # Method for solving for T(p) profile
 atmosphere_model            = 0         # Atmosphere model to be used, 0: JANUS | 1: AGNI
 atmosphere_solve_energy     = 0         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 

input/rce_mixed.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e4    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
@@ -75,6 +74,12 @@ steady_dprel                = 1.0e-9     # Percentage change in melt fraction ov
 emit_stop                   = 1         # Enable this break condition
 F_crit                      = 0.2       # Model will terminate when |F_atm| < F_crit
 
+# Atmospheric escape 
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
+
 # Method for solving for T(p) profile
 atmosphere_model            = 1         # Atmosphere model to be used, 0: JANUS | 1: AGNI
 atmosphere_solve_energy     = 1         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 

input/rce_steam.cfg

@@ -57,7 +57,6 @@ dt_initial                  = 1e4    # Inital step size
 # Flux convergence scheme and tolerances for surface equilibration
 shallow_ocean_layer         = 0         # 0: off | 1: on
 F_atm_bc                    = 0         # Boundary condition choice for F_atm, 0: TOA | 1: Surface
-RF_crit                     = 0.01      # depth fraction
 skin_d                      = 0.01      # m
 skin_k                      = 2.0       # W m-1 K-1
 prevent_warming             = 1         # Require that the planet only cool down over time, 0: disabled | 1: enabled
@@ -75,6 +74,11 @@ steady_dprel                = 1.0e-9     # Percentage change in melt fraction ov
 emit_stop                   = 1         # Enable this break condition
 F_crit                      = 0.2       # Model will terminate when |F_atm| < F_crit
 
+# Atmospheric escape 
+escape_model                = 0         # Escape model to be used, 0: None | 1: ZEPHYRUS | 2: Dummy
+escape_stop                 = 3e-4      # Terminate when atm mass drops below this fraction of its initial mass
+escape_dummy_rate           = 0.0       # Bulk escape rate for dummy escape model [kg s-1]
+
 # Method for solving for T(p) profile
 atmosphere_model            = 1         # Atmosphere model to be used, 0: JANUS | 1: AGNI
 atmosphere_solve_energy     = 1         # Enable time-stepped atmosphere solution, 0: disabled | 1: enabled 

plot/cpl_elements.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+
+from utils.modules_ext import *
+from utils.plot import *
+
+log = logging.getLogger("PROTEUS")
+
+def plot_elements( output_dir, plot_format="pdf", t0=100.0):
+
+    log.info("Plot elements")
+
+    hf_all = pd.read_csv(output_dir+"/runtime_helpfile.csv", sep=r"\s+")
+
+    time = np.array(hf_all["Time"] )
+    if len(time) < 3:
+        log.warning("Cannot make plot with less than 3 samples")
+        return
+
+    # make plot
+    lw = 1.2
+    al = 0.5
+    scale = 1.1
+    fig,ax = plt.subplots(1,1, figsize=(7*scale,4*scale))
+
+
+    total = np.zeros(len(time))
+    for e in element_list:
+        y = hf_all[e+"_kg_total"]
+        l = ax.plot(time, y, lw=lw, ls='solid', label="Total "+e)[0]
+
+        total += y
+
+        # c = l.get_color()
+        # ax.plot(time, hf_all[e+"_kg_liquid"], lw=lw, color=c, alpha=al, ls='dashed')  # in magma ocean
+        # ax.plot(time, hf_all[e+"_kg_atm"],    lw=lw, color=c, alpha=al, ls='dotted')  # in atmosphere
+
+    ax.plot(time, total,           lw=lw, ls='solid',  label='Total',  c='k')
+    ax.plot(time, hf_all["M_atm"], lw=lw, ls='dotted', label='Atmos.', c='k')
+
+    # decorate 
+    ax.set_ylabel("Inventory [kg]")
+    ax.set_yscale("log")
+    ax.set_xlabel("Time [yr]")
+    ax.set_xscale("log")
+    ax.set_xlim(left=t0, right=np.amax(time))
+    ax.grid(alpha=0.2)
+    ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
+
+    plt.close()
+    plt.ioff()
+
+    fpath = os.path.join(output_dir, "plot_elements.%s"%plot_format)
+    fig.savefig(fpath, dpi=200, bbox_inches='tight')
+
+#====================================================================
+def main():
+
+    if len(sys.argv) == 2:
+        cfg = sys.argv[1]
+    else:
+        cfg = 'init_coupler.cfg' 
+
+    # Read in COUPLER input file
+    log.info("Read cfg file")
+    from utils.coupler import ReadInitFile, SetDirectories
+    COUPLER_options, time_dict = ReadInitFile( cfg )
+
+    # Set directories dictionary
+    dirs = SetDirectories(COUPLER_options)
+
+    plot_elements( output_dir=dirs["output"], plot_format=COUPLER_options["plot_format"] )
+
+#====================================================================
+
+if __name__ == "__main__":
+
+    main()

plot/cpl_global.py

@@ -139,15 +139,15 @@ def plot_global( output_dir , COUPLER_options, logt=True, tmin=1e1):
     max_temp = np.amax(hf_all["T_surf"])
     ax_cl.plot(hf_all["Time"], hf_all["T_surf"], ls="dashed", lw=lw, alpha=al, color=dict_colors["int"])
     ax_cl.plot(hf_all["Time"], hf_all["T_surf"], ls="-",      lw=lw, alpha=al, color=dict_colors["atm"])
-    ax_cl.set_ylim(min(1000.0,min_temp) , max(3500.0,max_temp))
+    ax_cl.set_ylim(min(1000.0,min_temp-25) , max(3500.0,max_temp+25))
 
 
     # PLOT ax_bl
     ax_bl.axhline( y=COUPLER_options["planet_coresize"], ls='dashed', lw=lw*1.5, alpha=al, color=dict_colors["qmagenta_dark"], label=r'C-M boundary' )
     ax_bl.plot( hf_all["Time"], 1.0-hf_all["RF_depth"],   color=dict_colors["int"], ls="solid",    lw=lw, alpha=al, label=r'Rheol. front')
     ax_bl.plot( hf_all["Time"],     hf_all["Phi_global"], color=dict_colors["atm"], linestyle=':', lw=lw, alpha=al, label=r'Melt fraction')
     ax_bl.legend(loc='center left', **leg_kwargs)
-    ax_bl.set_ylim(0.0,1.0)
+    ax_bl.set_ylim(0.0,1.01)
 
 
     # PLOT ax_tr