Skip to content

GitLab

Commit 9a776365 authored by Laura Ketzer's avatar Laura Ketzer
Browse files

fixed multiprocessing issue for now -> newest running code in... 

fixed multiprocessing issue for now -> newest running code in Population_evolution_OwWu17__04_06-2020_FAST.ipynb
parent 3cb69307
Show whitespace changes
Inline Side-by-side
example_V1298Tau/V1298Tau_Paper_Calculations_and_Plots.ipynb
View file @ 9a776365
......@@ -3673,7 +3673,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
}
},
"nbformat": 4,
example_V1298Tau_github_copy/V1298Tau_Paper_Calculations_and_Plots.ipynb
View file @ 9a776365
......@@ -3739,7 +3739,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
}
},
"nbformat": 4,
platypos_package/Mass_evolution_function.py
View file @ 9a776365
......@@ -18,8 +18,8 @@ from Mass_loss_rate_function import mass_loss_rate_forward_Ot20
def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
initial_step_size, t_final, track_dict):
"""USED: 4th order Runge-Kutta as numerical integration method
Integrate from the current time (t_start (where planet has R0 and M0) into the future
taking into account photoevaporative mass loss.
Integrate from the current time (t_start (where planet has R0 and M0) into
the future taking into account photoevaporative mass loss.
Parameters:
-----------
......@@ -63,7 +63,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
f_env_0 = f_env = planet_object.fenv
R0 = R = planet_object.radius
M0 = M = planet_object.mass
rho0 = rho = plmo14.density_planet(M0, R0)
rho0 = rho = plmoLoFo14.density_planet(M0, R0)
M_env0 = M_env = M0 - planet_object.core_mass
M_core = planet_object.core_mass
R_core = planet_object.core_radius
......@@ -105,7 +105,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# complete atmospheric removal
while t <= t_final:
#print("i - t - dt: ", i, t, dt)
#print(i, " t= ", t, dt)
# This step (Lx(t) calculation) is just for me to trace Lx and check if
# it is correct. It is NOT required since the Lx(t) calculation is
......@@ -141,7 +141,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
k1 = (dt*Myr_to_sec * Mdot1)/M_earth
M_05k1 = M + 0.5 * k1 # mass after 1st RK step
M_env_05k1 = M_05k1 - M_core
#f_env_05k1 = (M_env_05k1/M_05k1) * 100 # new envelope mass fraction
f_env_05k1 = (M_env_05k1/M_05k1) * 100 # new envelope mass fraction
if (i == 1) and (M_05k1 < M_core):
# then I am still in the first RK iteration, and the initial
# step size was likely too large -> set step size to minumum
......@@ -154,7 +154,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
k2 = (dt*Myr_to_sec * Mdot2)/M_earth
M_05k2 = M + 0.5 * k2
M_env_05k2 = M_05k2 - M_core
#f_env_05k2 = (M_env_05k2/M_05k2) * 100
f_env_05k2 = (M_env_05k2/M_05k2) * 100
if (i == 1) and (M_05k2 < M_core):
# then I am still in the first RK iteration, and the initial
# step size was likely too large -> set step size to minumum
......@@ -167,6 +167,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
k3 = (dt*Myr_to_sec * Mdot3)/M_earth
M_k3 = M + k3
M_env_k3 = M_k3 - M_core
f_env_k3 = (M_env_k3/M_k3) * 100
if (i == 1) and (M_k3 < M_core):
# then I am still in the first RK iteration, and the initial
# step size was likely too large -> set step size to minumum
......@@ -186,8 +187,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# now it is time to check, if atmosphere is gone or
# if planet is close to complete atmosphere removal
if ((np.isnan(M_lost) == True) or (M_new <= M_core))
and (dt == min_step_size):
if ((np.isnan(M_lost) == True) or (M_new <= M_core)) and (dt == min_step_size):
# if M_lost = nan (i.e. planet evaporates in one of the RK
# steps) OR the four RK steps finish and the new planet mass is
# smaller or equal to the core mass, then the planet counts as
......@@ -198,8 +198,8 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# t_i+dt; this terminates the code and returns the final planet
# properties
# print("Atmosphere has evaportated! Only bare rocky core left!\
# STOP this madness!")
#print("Atmosphere has evaportated! Only bare rocky core left!"\
# + " STOP this madness!")
# since the the stop criterium is reached, we assume at t_i+1
# the planet only consists of the bare rocky core with the
......@@ -212,8 +212,8 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
envelope_left = False # set flag for complete env. removal
break
elif ((np.isnan(M_lost) == True) or (M_new <= M_core))
and (dt > min_step_size) and (close_to_evaporation == False):
elif ((np.isnan(M_lost) == True) or (M_new <= M_core)) and (dt > min_step_size) and (close_to_evaporation == False):
#print("close to evaporation")
# planet close to evaporation, but since the step size is not
# minimum yet, we set it to its minimum value and run the RK
# iteration again (until above stopping condition is fulfilled)
......@@ -231,14 +231,16 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# new radius and check how drastic the radius change would be;
# adjust the step size if too drastic or too little
f_env_new = (M_env_new/M_new)*100 # in %
R_new = plmo14.calculate_planet_radius(M_core, f_env_new, t,
R_new = plmoLoFo14.calculate_planet_radius(M_core, f_env_new, t,
flux_at_planet_earth(
planet_object.Lbol,
planet_object.distance),
planet_object.metallicity)
#print("R_new, f_new: ", R_new, f_env_new)
# only adjust step size if planet is not close to complete evaporat.
if (close_to_evaporation == False):
#print("radius check")
# then do the check on how much the radius changes
# R(t_i) compared to R(t_i+dt);
# if radius change is larger than 1%, make step size smaller
......@@ -250,8 +252,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
R_change = abs((R-R_new)/R)*100 # radius change compared to
# previous radius - in percent
if (R_change > 0.1) and (t < track_dict["t_curr"])
and (dt > min_step_size):
if (R_change > 0.5) and (t < track_dict["t_curr"]) and (dt > min_step_size):
dt = dt / 10.
break
......@@ -259,22 +260,30 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# dt = dt / 10.
# break
elif (R_change < (0.01)) and (t < track_dict["t_curr"])
and (dt < max_step_size):
elif (R_change < (0.01)) and (t < track_dict["t_curr"]) and (dt < max_step_size):
dt = dt * 10.
break
##################################################################################
# need to make sure that code does not end up in infinite loop
# if I chode my limits too close to each other, in a 0.1 Myr time
# step the radius change might bee too big, but in a 0.01 Myr time
# step it it too small -> then the code is stuck.
# in such situation I could continue with the smaller step size or chose
# sth in between.
##################################################################################
# in principle I can adjust the code such that these hardcoded
# parameters are different for early planet evolution where
# much more is happening typically, and late planet evolution
# where almost no change is occurring anymore
elif (R_change > 0.1) and (t >= track_dict["t_curr"])
and (dt > min_step_size):
elif (R_change > 0.5) and (t >= track_dict["t_curr"]) and (dt > min_step_size):
dt = dt / 10.
break
elif (R_change < (0.01)) and (t >= track_dict["t_curr"])
and (dt < max_step_size):
elif (R_change < (0.01)) and (t >= track_dict["t_curr"]) and (dt < max_step_size):
dt = dt * 10
break
......@@ -295,7 +304,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# calculate new radius with new planet mass/envelope
# mass fraction & one time step later
R = plmo14.calculate_planet_radius(M_core, f_env, t,
R = plmoLoFo14.calculate_planet_radius(M_core, f_env, t,
flux_at_planet_earth(
planet_object.Lbol,
planet_object.distance),
......@@ -324,7 +333,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
# calculate new radius with new planet mass/envelope mass
# fraction & one time step later
R = plmo14.calculate_planet_radius(M_core, f_env, t,
R = plmoLoFo14.calculate_planet_radius(M_core, f_env, t,
flux_at_planet_earth(
planet_object.Lbol,
planet_object.distance),
......@@ -338,7 +347,7 @@ def mass_planet_RK4_forward_LO14(epsilon, K_on, beta_on, planet_object,
if (envelope_left == False):
# planet has evaporated, so return last planet params for bare core
return np.array(t_arr), np.array(M_arr),
return np.array(t_arr), np.array(M_arr),\
np.array(R_arr), np.array(Lx_arr)
#print("Done!")
......@@ -379,17 +388,17 @@ def mass_planet_RK4_forward_LO14_PAPER(epsilon, K_on, beta_on, planet_object, in
f_env_0 = f_env = planet_object.fenv
R0 = R = planet_object.radius # should match observed radius - determined by M_core and f_env
M0 = M = planet_object.mass
rho0 = rho = plmo14.density_planet(M0, R0) # initial mean density
rho0 = rho = plmoLoFo14.density_planet(M0, R0) # initial mean density
M_env0 = M_env = M0 - planet_object.core_mass # initial envelope mass
M_core = planet_object.core_mass
# specify beta0 and K0
if beta_on == "yes": # use the beta estimate from Salz et al. 2016
beta = beta0 = bk.beta_fct_LO14(M0, Fxuv0, R0)
beta = beta0 = bk.beta_fct(M0, Fxuv0, R0)
elif beta_on == "no":
beta = beta0 = 1.
if K_on == "yes": # use K-correction estimation from Erkaev et al. 2007
K = K0 = bk.K_fct_LO14(planet_object.distance, M0, planet_object.mass_star, R0)
K = K0 = bk.K_fct(planet_object.distance, M0, planet_object.mass_star, R0)
elif K_on == "no":
K = K0 = 1.
......@@ -462,7 +471,7 @@ def mass_planet_RK4_forward_LO14_PAPER(epsilon, K_on, beta_on, planet_object, in
# new envelope mass fraction:
f_env = (M_env/M)*100 # in %
# calculate new radius with new planet mass/envelope mass fraction & one time step later
R_arr[i+1] = R = plmo14.calculate_planet_radius(M_core, f_env, t, flux_at_planet_earth(planet_object.Lbol,
R_arr[i+1] = R = plmoLoFo14.calculate_planet_radius(M_core, f_env, t, flux_at_planet_earth(planet_object.Lbol,
planet_object.distance), planet_object.metallicity)
else:
......@@ -534,11 +543,11 @@ def mass_planet_RK4_forward_Ot14(epsilon, K_on, beta_on, planet_object, initial_
# specify beta0 and K0
if beta_on == "yes": # use the beta estimate from Salz et al. 2016
beta = beta0 = bk.beta_fct_LO14(M0, Fxuv0, R0)
beta = beta0 = bk.beta_fct(M0, Fxuv0, R0)
elif beta_on == "no":
beta = beta0 = 1.
if K_on == "yes": # use K-correction estimation from Erkaev et al. 2007
K = K0 = bk.K_fct_LO14(planet_object.distance, M0, planet_object.mass_star, R0)
K = K0 = bk.K_fct(planet_object.distance, M0, planet_object.mass_star, R0)
elif K_on == "no":
K = K0 = 1.
......@@ -682,11 +691,11 @@ def mass_planet_RK4_forward_Ot14_PAPER(epsilon, K_on, beta_on, planet_object, in
# specify beta0 and K0
if beta_on == "yes": # use the beta estimate from Salz et al. 2016
beta = beta0 = bk.beta_fct_LO14(M0, Fxuv0, R0)
beta = beta0 = bk.beta_fct(M0, Fxuv0, R0)
elif beta_on == "no":
beta = beta0 = 1.
if K_on == "yes": # use K-correction estimation from Erkaev et al. 2007
K = K0 = bk.K_fct_LO14(planet_object.distance, M0, planet_object.mass_star, R0)
K = K0 = bk.K_fct(planet_object.distance, M0, planet_object.mass_star, R0)
elif K_on == "no":
K = K0 = 1.
......
platypos_package/Planet_class_LoFo14-delete_once_PEP8_formatting_successfully_done.py
View file @ 9a776365
......@@ -216,7 +216,7 @@ class planet_LoFo14():
#print("Saved!\n")
# make another file, which contains the final parameters
if os.path.exists(path_for_saving+planet_folder_id+"_"+self.planet_id+"_final.txt"):
if os.path.exists(path_for_saving+"_"+self.planet_id+"_final.txt"):
pass
else:
p = open(path_for_saving+self.planet_id+"_final.txt", "a")
......
platypos_package/Planet_class_LoFo14.py
View file @ 9a776365
import os
import numpy as np
import pandas as pd
from scipy.optimize import fsolve
import scipy.optimize as optimize
import astropy.units as u
from astropy import constants as const
import scipy.optimize as optimize
import os
import pandas as pd
from Lx_evo_and_flux import Lx_evo
from Lx_evo_and_flux import flux_at_planet_earth
from Lx_evo_and_flux import L_xuv_all
......@@ -65,8 +66,8 @@ class planet_LoFo14():
try:
# check if envelope mass fraction is specified, then Case 1
planet_dict["fenv"]
self.planet_info = "Case 1 - artificial planet \
(with M_core & f_env)"
self.planet_info = "Case 1 - artificial planet"\
+ " (with M_core & f_env)"
# Case 1: artificial planet with fenv & M_core given, need to
# calculate the total mass and radius
self.fenv = planet_dict["fenv"]
......@@ -84,9 +85,9 @@ class planet_LoFo14():
# Case 3: An observed planet with radius and mass
# measurement, plus core mass is specified;
# need to calculate/estimate envelope mass frac.
self.planet_info = "Case 3 - obs. planet with radius & \
mass measurement (and core mass \
estimate)"
self.planet_info = "Case 3 - obs. planet with radius"\
+ " & mass measurement (and core "\
+ "mass estimate)"
self.core_mass = planet_dict["core_mass"]
self.mass = planet_dict["mass"]
self.radius = planet_dict["radius"]
......@@ -100,8 +101,8 @@ class planet_LoFo14():
break
except KeyError:
# no mass and fenv given -> Case 2
self.planet_info = "Case 2 - obs. planet with radius, \
but no mass measurement"
self.planet_info = "Case 2 - obs. planet with"\
+ " radius, but no mass measurement"
# Case 2 - observed planet with a without a mass, but
# core mass estimate, need to calculate fenv
self.core_mass = planet_dict["core_mass"]
......@@ -169,10 +170,14 @@ class planet_LoFo14():
""" Function to set the right planet name based on the track specified.
This can then be used to check if a particular planet on a particular
track has already evolved (i.e. if outpufile exists). """
self.planet_id = 'planet_a' + str(np.round(self.distance, 3)).replace('.', 'dot')\
+ '_Mcore' + str(np.round(self.core_mass, 3)).replace(".", "dot")\
+ '_fenv' + str(np.round(self.fenv, 3)) + '_' + self.metallicity\
+ '_Mstar' + str(np.round(self.mass_star, 3)).replace(".", "dot")\
self.planet_id = 'planet_a'\
+ str(np.round(self.distance, 3)).replace('.', 'dot')\
+ '_Mcore'\
+ str(np.round(self.core_mass, 3)).replace(".", "dot")\
+ '_fenv'\
+ str(np.round(self.fenv, 3)) + '_' + self.metallicity\
+ '_Mstar'\
+ str(np.round(self.mass_star, 3)).replace(".", "dot")\
+ "_K_" + K_on + "_beta_" + beta_on\
+ "_track_" + str(evo_track_dict["t_start"]) + "_"\
+ str(evo_track_dict["t_sat"]) + "_" + str(t_final)\
......@@ -202,13 +207,13 @@ class planet_LoFo14():
# planet already exists
self.has_evolved = True
else:
print("Planet: ", self.planet_id+".txt")
#print("Planet: ", self.planet_id+".txt")
# Next, create a file (e.g. planet_XXXX.txt) which contains the
# initial planet params
if os.path.exists(path_for_saving+planet_folder_id+".txt"):
pass
else:
p = open(path_for_saving+planet_folder_id+".txt", "a")
p = open(path_for_saving+planet_folder_id+".txt", "w")
planet_params = "a,core_mass,fenv,mass,radius,metallicity,age\n"\
+ str(self.distance) + "," + str(self.core_mass)\
+ "," + str(self.fenv) + "," + str(self.mass)\
......@@ -224,9 +229,9 @@ class planet_LoFo14():
pass
else:
t = open(path_for_saving+"track_params_" +
self.planet_id+".txt", "a")
track_params = "t_start,t_sat,t_curr,t_5Gyr,Lx_max,Lx_curr,\
Lx_5Gyr,dt_drop,Lx_drop_factor\n"\
self.planet_id+".txt", "w")
track_params = "t_start,t_sat,t_curr,t_5Gyr,Lx_max,Lx_curr,"\
+ "Lx_5Gyr,dt_drop,Lx_drop_factor\n"\
+ str(evo_track_dict["t_start"]) + ","\
+ str(evo_track_dict["t_sat"]) + "," \
+ str(evo_track_dict["t_curr"]) + ","\
......@@ -243,7 +248,7 @@ class planet_LoFo14():
if os.path.exists(path_for_saving+"host_star_properties.txt"):
pass
else:
s = open(path_for_saving+"host_star_properties.txt", "a")
s = open(path_for_saving+"host_star_properties.txt", "w")
star_params = "star_id,mass_star,radius_star,age,Lbol,Lx_age\n"\
+ self.star_id + "," + str(self.mass_star) + ","\
+ str(self.radius_star) + "," + str(self.age)\
......@@ -267,11 +272,11 @@ class planet_LoFo14():
df.to_csv(path_for_saving+self.planet_id+".txt", index=None)
# create another file, which contains the final parameters only
if os.path.exists(path_for_saving+planet_folder_id+"_"+\
if os.path.exists(path_for_saving+\
self.planet_id+"_final.txt"):
pass
else:
p = open(path_for_saving+self.planet_id+"_final.txt", "a")
p = open(path_for_saving+self.planet_id+"_final.txt", "w")
# get index of last valid entry in the radius array and access
# its value
index_of_last_entry = df["Radius"][df["Radius"].notna()].index[-1]
......@@ -307,4 +312,4 @@ class planet_LoFo14():
def evolve_backwards(self, t_final, initial_step_size, epsilon, K_on,
beta_on, evo_track_dict, path_for_saving):
print("Not implemented yet.")
continue
platypos_package/Planet_model_Ot20.py
View file @ 9a776365
......@@ -20,12 +20,12 @@ def calculate_mass_planet_Ot19(R_pl):
rho_volatile = (M_p_volatile*M_earth) \
/ (4/3*np.pi*(R_pl*R_earth)**3)
if (rho_volatile >= 3.3):
raise Exception("Planet with this radius is too small and likely \
rocky; use LoFo14 models instead.")
raise Exception("Planet with this radius is too small and"\
+ " likely rocky; use LoFo14 models instead.")
else:
if (M_p_volatile >= 120):
raise Exception("Planet too massive. M-R relation only valid \
for <120 M_earth.")
raise Exception("Planet too massive. M-R relation only valid"\
+ " for <120 M_earth.")
else:
return M_p_volatile
......@@ -61,12 +61,12 @@ def calculate_radius_planet_Ot19(M_pl):
rho_volatile = (M_pl*M_earth) \
/ (4/3*np.pi*(R_p_volatile*R_earth)**3)
if (rho_volatile >= 3.3):
raise Exception("Planet with this mass/radius is too small and \
likely rocky; use LoFo14 models instead.")
raise Exception("Planet with this mass/radius is too small and"\
+ " likely rocky; use LoFo14 models instead.")
else:
if (M_pl >= 120):
raise Exception("Planet too massive. M-R relation only \
valid for <120 M_earth.")
raise Exception("Planet too massive. M-R relation only"\
+ " valid for <120 M_earth.")
else:
return R_p_volatile
......
platypos_package/Planet_models_LoFo14.py
View file @ 9a776365
......@@ -4,8 +4,8 @@ import warnings
import astropy.units as u
from astropy import constants as const
# import warnings
# warnings.filterwarnings("ignore", category=RuntimeWarning)
import warnings
warnings.filterwarnings("ignore", category=RuntimeWarning)
# ignoring this warining is certainly not the best way, but it is currently
# thrown when one of the "in-between" time steps inside the Runge-Kutta
# integration method results in a planet which has no atmosphere left.
......
platypos_package/Write_to_file_function.py
View file @ 9a776365
# function to write to file
def write_results_to_file(t_arr1, M_arr1, R_arr1, Lx_arr1,
t_arr2, M_arr2, R_arr2, Lx_arr2,
t_arr3, M_arr3, R_arr3, Lx_arr3,
radius_planet, path, filename):
"""col 1-4 is track 1, col 5-8 is track 2 and col 9-12 is track 3"""
df1 = pd.DataFrame({"Time1": t_arr1, "Mass1": M_arr1, "Radius1": radius_planet(M_arr1), "Lx1": Lx_arr1})
df2 = pd.DataFrame({"Time2": t_arr2, "Mass2": M_arr2, "Radius2": radius_planet(M_arr2), "Lx2": Lx_arr2})
df3 = pd.DataFrame({"Time3": t_arr3, "Mass3": M_arr3, "Radius3": radius_planet(M_arr3), "Lx3": Lx_arr3})
"""function to write results to file (outdated); col 1-4 is track 1,
col 5-8 is track 2 and col 9-12 is track 3"""
df1 = pd.DataFrame({"Time1": t_arr1, "Mass1": M_arr1, \
"Radius1": radius_planet(M_arr1), \
"Lx1": Lx_arr1})
df2 = pd.DataFrame({"Time2": t_arr2, "Mass2": M_arr2, \
"Radius2": radius_planet(M_arr2), \
"Lx2": Lx_arr2})
df3 = pd.DataFrame({"Time3": t_arr3, "Mass3": M_arr3, \
"Radius3": radius_planet(M_arr3), \
"Lx3": Lx_arr3})
result = pd.concat([df1, df2, df3], axis=1, sort=False)
result.to_csv(path+filename)
return None
\ No newline at end of file
population_evolution/Platypos_RUNS/result_files_1.0_to_3000.0Myr_smass_cks_Mcore3_beta_no_K_no_LxTu15_different_tracks_newestLximplementation/planet_0002/host_star_properties.txt 0 → 100644
View file @ 9a776365
star_id,mass_star,radius_star,age,Lbol,Lx_age
star_age1.0_mass1.15,1.1493877759414373,None,1.0,1.8695398206195215,4.588922130517988e+30
\ No newline at end of file
population_evolution/Platypos_RUNS/result_files_1.0_to_3000.0Myr_smass_cks_Mcore3_beta_no_K_no_LxTu15_different_tracks_newestLximplementation/planet_0002/planet_0002.txt 0 → 100644
View file @ 9a776365
a,core_mass,fenv,mass,radius,metallicity,age
0.10549918688768402,4.078595745230332,4.5321547457624165,4.27221933664549,6.001359676637803,solarZ,1.0
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment