Update tool SGWB to 0.0.1+galaxy0

tools/sgwb/GW_spectrum.py

@@ -0,0 +1,369 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[ ]:
+
+
+import json
+import os
+import shutil
+import sys
+
+try:
+    import numpy as np
+    _numpy_available = True
+except ImportError:
+    _numpy_available = False
+
+try:
+    from oda_api.json import CustomJSONEncoder
+except ImportError:
+    from json import JSONEncoder as CustomJSONEncoder
+
+_galaxy_wd = os.getcwd()
+
+
+# In[13]:
+
+
+# we first load necessary packages
+import numpy as np
+import matplotlib
+import matplotlib.pyplot as plt
+from matplotlib.colors import LogNorm
+get_ipython().run_line_magic('matplotlib', 'inline')
+from numpy import log, pi, sqrt
+import astropy.constants as const
+from astropy.constants import c
+import astropy.units as u
+import pandas as pd
+from random import seed
+from random import random
+import plotly.graph_objs as go
+from scipy.spatial import ConvexHull
+from scipy.integrate import quad
+from math import *
+
+from oda_api.data_products import PictureProduct
+from oda_api.data_products import ODAAstropyTable
+
+
+# In[14]:
+
+
+# Parameters of the phase transition
+# Temperature in GeV
+T_star=0.3 #http://odahub.io/ontology#Energy_GeV
+
+# Numbers of relativistic degrees of freedom
+g_star=50 # http://odahub.io/ontology#Integer
+#g_star_s=50 # http://odahub.io/ontology#Integer
+
+# beta/H : rate of the phase transition compared to Hubble rate
+beta_H=1.    
+
+# ratio of the energy density deposited in the bubbles to the radiation energy density
+alpha=1       # http://odahub.io/ontology#Float 
+
+# fraction of turbulent energy that goes to gw N.B. arXiv:1004.4187 claims that epsilon_turb=0.05, but checks below show that it is rather 0.01
+epsilon_turb=1.0 # http://odahub.io/ontology#Float 
+
+# terminal velocity of bubbles
+v_w=0.99  # http://odahub.io/ontology#Float  
+
+
+# In[ ]:
+
+
+with open('inputs.json', 'r') as fd:
+    inp_dic = json.load(fd)
+if '_data_product' in inp_dic.keys():
+    inp_pdic = inp_dic['_data_product']
+else:
+    inp_pdic = inp_dic
+
+for vn, vv in inp_pdic.items():
+    if vn != '_selector':
+        globals()[vn] = type(globals()[vn])(vv)
+
+
+# Theo, please specify the units of $H_0$ in the cell below
+
+# In[15]:
+
+
+T_star=T_star*u.GeV
+T0=2.73  #Temperature of the universe now in Kelvin
+conversion=8.617*10**(-9-5)  #conversion factor from kelvin to GeV
+H0=3.086*10**(22)    #current Hubble rate 
+h=0.7          # dimensionless Hubble Constant
+c_s=3**(-0.5)  #speed of sound
+
+
+# In[16]:
+
+
+#Eq.20 of arXiv:1512.06239, corrected according to Appendix A of arXiv:1004.4187
+def ka_v(alpha_v,v):
+    zeta=((2./3.*alpha_v+alpha_v**2)**0.5+(1/3.)**0.5)/(1+alpha_v)
+    kappa_a=6.9*v**(6./5.)*alpha_v/(1.36-0.037*alpha_v**0.5+alpha_v)
+    kappa_b=alpha_v**(2./5.)/(0.017+(0.997+alpha_v)**(2./5.))
+    kappa_c=alpha_v**0.5/(0.135+(0.98+alpha_v)**0.5)
+    kappa_d=alpha_v/(0.73+0.083*alpha_v**0.6+alpha_v)
+    deltak=-0.9*log(alpha_v**0.5/(1+alpha_v**0.5))
+    if(v<c_s):
+        return c_s**(11./5.)*kappa_a*kappa_b/((c_s**(11./5.)-v**(11./5.))*kappa_b+v*c_s**(6./5.)*kappa_a)
+    elif(v>zeta):
+        return (zeta-1)**3*(zeta/v)**(5./2)*kappa_c*kappa_d/(((zeta-1)**3-(v-1)**3)*zeta**(5./2.)*kappa_c+(v-1)**3*kappa_d)
+    else:
+        return kappa_b+(v-c_s)*deltak+(v-c_s)**3/(zeta-c_s)**3*(kappa_c-kappa_b-(zeta-c_s)*deltak)
+kappa_v=ka_v(alpha,v_w)
+kappa_therm=(1-kappa_v)  
+print('Bubble wall limiting velocity:',v_w)
+print('Fraction of released energy in bulk motion:',kappa_v,', Thermal energy fraction:',kappa_therm)
+Omega_star=(kappa_v)*alpha/(1+alpha)
+print('Omega in bulk motion:', Omega_star)
+
+
+# In[17]:
+
+
+#Comoving Hubble rate at the phase transition Eq. 11 of arXiv:1512.06239
+
+def H_star_bis(T_star):
+    return 16.5e-6*(T_star/(100.*u.GeV))*(g_star/100)**(1./6.)*u.Hz
+
+#With factor of 2pi with definition of scale factor and Hubble rate
+def H_star(T_star):
+    scale=T0*conversion*u.GeV/(T_star*(g_star)**(1/3.))
+    Hexp=((4.7*10**(-42)*g_star)**(1/2)*(T_star/(conversion*u.GeV))**2)*u.Hz
+    return scale*Hexp/(2*pi)
+
+
+R_H_star=(const.c/H_star(T_star)).to(u.Mpc)
+
+print('Reference frequency:',H_star(T_star),', Horizon size:',R_H_star)
+
+lambda_star=((8*pi)**(1/3)*max([v_w,c_s])/(beta_H*H_star(T_star))*c)   # size of bubbles at percolation in units of Hubble scale
+#there are different distance scales that we can define 
+
+R_star=lambda_star # size of bubbles at percolation (?) in units of Hubble scale
+Delta_w=sqrt((v_w-c_s)**2)/v_w  # <1, the width of the bubble wall in units of R_star
+R_peak=Delta_w*R_star           # the GW spectrum peaks ad the frequency correspoding to the bubble wall width
+print('light crossing distance on for the duration of phase transition:',lambda_star, ', bubble size at percolation:',R_star)
+
+
+# In[18]:
+
+
+#Ellis definition of GW_spectrum with broken power law
+
+def GW_old(f,T_star,alpha,beta_H,v_w):
+    A=5.1*10**(-2)
+    a=2.4
+    b=2.4
+    c=4.
+    delta=1.0
+    scale=T0*conversion*u.GeV/(T_star*(g_star)**(1/3.))
+    #Hubble rate from Friedman
+    Hexp=((4.7*10**(-42)*g_star)**(1/2)*(T_star/(conversion*u.GeV))**2)*u.Hz
+    fH=Hexp*scale/(2*pi)
+    Sh=(1+(f/fH)**((-3+a)/delta))**(-delta)
+    fp=0.7*fH*beta_H
+    factor=scale**4*(Hexp/(70*10**(3)/(H0)*u.Hz))**2
+    return (beta_H)**2*A*(a+b)**c*Sh/(b*(f/fp)**(-a/c)+a*(f/fp)**(b/c))**c*factor
+
+
+
+# In[19]:
+
+
+# HL model formula
+
+def GW_sound2(f,T_star,alpha,beta_H,v_w):
+    #f=f*u.Hz
+    R_H_star=(const.c/H_star(T_star)).to(u.Mpc)
+    kappa_v=ka_v(alpha,v_w) 
+    Omega_star=(kappa_v)*alpha/(1+alpha)
+    Omega_gw_tilde=10**(-2)   #new parameter (that comes from simulations apparently)
+    lambda_star=((8*pi)**(1/3)*max([v_w,c_s])/(beta_H*H_star(T_star))*c)   #characteristic light-crossing distance scale                                        
+    Delta_w=sqrt((v_w-c_s)**2)/v_w  # <1, the width of the bubble wall in units of R_star
+    s=Delta_w*lambda_star*f/c          # the GW spectrum peaks ad the frequency correspoding to the bubble wall width
+  # frequencies are measured in units of the peak frequency
+    s1=lambda_star*f/c
+    r_b=Delta_w                     # apparently, there are two different notations for the same 
+    m=(9*r_b**4+1)/(r_b**4+1)
+    M=16*(1+r_b**(-3))**(2/3.)*(r_b*s1)**3/((1+s1**3)**(2./3.)*(3+s**2)**2)
+    mu=4.78-6.27*r_b+3.34*r_b**2
+    B_cursive= Omega_gw_tilde/mu           #new parameter
+    factor=(Omega_star*lambda_star*H_star(T_star)/c)**2/(Omega_star**(1/2.)+lambda_star*H_star(T_star)/c)
+    old_factor=3*B_cursive*factor*1.64*10**(-5)*(100/g_star)**(1/3.)*v_w/h**2 
+    return (old_factor*M).cgs
+
+
+# In[20]:
+
+
+#   SSM model formula
+
+def GW_sound1(f,T_star,alpha,beta_H,v_w):
+    #f=f*u.Hz
+    R_H_star=(const.c/H_star(T_star)).to(u.Mpc)
+    kappa_v=ka_v(alpha,v_w) 
+    Omega_star=(kappa_v)*alpha/(1+alpha)
+    Omega_gw_tilde=10**(-2)   #new parameter (that comes from simulations apparently)
+    lambda_star=((8*pi)**(1/3)*max([v_w,c_s])/(beta_H*H_star(T_star))*c)   #characteristic light-crossing distance scale                                        
+    Delta_w=sqrt((v_w-c_s)**2)/v_w  # <1, the width of the bubble wall in units of R_star
+    s=Delta_w*lambda_star*f/c          # the GW spectrum peaks ad the frequency correspoding to the bubble wall width                    # frequencies are measured in units of the peak frequency
+    m=(9*Delta_w**4+1)/(Delta_w**4+1)
+    M=s**9*((Delta_w**4+1)/(Delta_w**4+((s)**4)))**2*(5/(5-m+m*(s)**2))**(5./2.)
+    mu=4.78-6.27*Delta_w+3.34*Delta_w**2
+    B_cursive= Omega_gw_tilde/mu           #new parameter
+    factor=(Omega_star*lambda_star*H_star(T_star)/c)**2/(Omega_star**(1/2.)+lambda_star*H_star(T_star)/c)
+    old_factor=3*B_cursive*factor*1.64*10**(-5)*(100/g_star)**(1/3.)*v_w/h**2 
+    return (old_factor*M).cgs
+
+
+
+
+# In[21]:
+
+
+# Eq 1 of the new Overleaf, from Alberto
+
+def GW_turb1(f,T_star,alpha,beta_H,v_w,epsilon_turb):
+    R_H_star=(const.c/H_star(T_star)).to(u.Mpc)
+    kappa_v=ka_v(alpha,v_w) 
+    Omega_star=(kappa_v)*alpha/(1+alpha)
+    lambda_star=(((8*pi)**(1/3)*max([v_w,c_s])/(beta_H*H_star(T_star)))*c) #characteristic light-crossing distance scale 
+
+    Delta_w=sqrt((v_w-c_s)**2)/v_w  # <1, the width of the bubble wall in units of R_star
+    R_peak=Delta_w*lambda_star           # the GW spectrum peaks ad the frequency correspoding to the bubble wall width
+    u_star=sqrt(0.75*epsilon_turb*Omega_star) # alfven velocity
+    dt_fin=(2*lambda_star/u_star/c) #eddy processing time
+
+    T_GW=np.log10(1+(H_star(T_star)*dt_fin/(2*pi)))*(f<1/dt_fin)+np.log10(1+(H_star(T_star)/(2*pi*f)))*(f>=1/dt_fin)
+    T_GW=T_GW**2
+    alpha_pi=2.15
+    P_pi=(1+((lambda_star*f)/(2.2*c))**alpha_pi)**(-11/(3*alpha_pi))
+    M=(lambda_star*f/c)**3*(4*pi**2*T_GW*P_pi)/(0.84*(lambda_star*H_star(T_star)/c)**2)
+    res=3*(1.75 * 10**(-3))*(Omega_star*epsilon_turb)**2*(lambda_star*H_star(T_star)/c)**2*1.64*10**(-5)*(100/g_star)**(1/3.)/h**2
+    return (res*M)
+
+
+
+# In[28]:
+
+
+#Range of frequencies used
+
+f=np.logspace(-10,-2,50)*u.Hz
+
+lambda_star=((8*pi)**(1/3)*max([v_w,c_s])/(beta_H*H_star(T_star))*c)
+kappa_v=ka_v(alpha,v_w)   #kappa_therm=(1-kappa_v)  
+Omega_star=(kappa_v)*alpha/(1+alpha)
+u_star=sqrt(0.75*epsilon_turb*Omega_star) # alfven velocity
+dt_fin=(2*lambda_star/u_star/c) 
+Delta_w=sqrt((v_w-c_s)**2)/v_w
+delta=1.0
+scale=T0*conversion*u.GeV/(T_star*(g_star**(1/3.)))
+Hexp=((4.7*10**(-42)*g_star)**(1/2)*(T_star/(conversion*u.GeV))**2)*u.Hz
+fH=Hexp*scale/(2*pi)
+fp=0.7*fH*beta_H
+
+
+#Printing the spectrums
+
+spectrum_turb=GW_turb1(f,T_star,alpha,beta_H,v_w,epsilon_turb)
+plt.plot(f,spectrum_turb,label='turbulence',color='blue',linewidth=4,linestyle='dotted')
+spectrum_sound=GW_sound2(f,T_star,alpha,beta_H,v_w)
+
+spectrum_old=GW_old(f,T_star,alpha,beta_H,v_w)
+plt.plot(f,spectrum_sound,label='sound waves',color='red',linewidth=4,linestyle='dashed')
+plt.plot(f,spectrum_sound+spectrum_turb,color='grey',linewidth=4,label='total')
+#plt.plot(f,spectrum_old,color='purple',linewidth=4,label='total')
+
+
+#plt.axvline(1/(dt_fin*u.Hz).cgs,linestyle='dashed',color='black',label=r'$dt_{fin}**(-1)$')
+#plt.axvline((c/lambda_star/u.Hz).cgs,linestyle='dotted',color='black',label=r'$c/\lambda_*$')
+#plt.axvline((c/(Delta_w*lambda_star)/u.Hz).cgs,linestyle='dashdot',color='black',label=r'$c/(\Delta_w \lambda_*)$')
+#plt.axvline(c/(R_peak*u.Hz),linestyle='dashed',color='blue',label='peak')
+
+plt.legend()
+
+#Butterfly of compatibility with the NANOgrav data
+
+butterfly2=np.array([[8.533691739758777e-8,0.0000016780550400704105],[8.361136018023004e-8,1.0740085826829729e-7],[8.499066585218291e-9,3.882820258009008e-9],[1.029481229115365e-9,3.6152599901104956e-11],[1.0353166841868053e-9,2.766052794917924e-10],[7.3944540651210095e-9,6.632930188159042e-9]])
+plt.fill(butterfly2[:,0],butterfly2[:,1])
+plt.xscale('log')
+plt.yscale('log')
+plt.xlabel('$f$, Hz')
+plt.ylabel('$h_0^2\Omega_{gw}(f)$')
+plt.savefig('Spectrum.png',format='png',bbox_inches="tight")
+
+
+# In[29]:
+
+
+bin_image = PictureProduct.from_file('Spectrum.png')
+from astropy.table import Table
+data=[f,spectrum_sound,spectrum_turb]
+names=('f[Hz]','Omega_sound_waves[MJD]','Omega_turbulence[MJD]')
+spectrum = ODAAstropyTable(Table(data, names = names))
+
+
+# In[30]:
+
+
+picture = bin_image # http://odahub.io/ontology#ODAPictureProduct
+spectrum_astropy_table = spectrum # http://odahub.io/ontology#ODAAstropyTable
+
+
+# In[ ]:
+
+
+
+
+
+# In[ ]:
+
+
+_simple_outs, _oda_outs = [], []
+_galaxy_meta_data = {}
+_oda_outs.append(('out_GW_spectrum_picture', 'picture_galaxy.output', picture))
+_oda_outs.append(('out_GW_spectrum_spectrum_astropy_table', 'spectrum_astropy_table_galaxy.output', spectrum_astropy_table))
+
+for _outn, _outfn, _outv in _oda_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    elif getattr(_outv, "write_fits_file", None):
+        _outv.write_fits_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': 'fits'}
+    elif getattr(_outv, "write_file", None):
+        _outv.write_file(_galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd, cls=CustomJSONEncoder)
+        _galaxy_meta_data[_outn] = {'ext': 'json'}
+
+for _outn, _outfn, _outv in _simple_outs:
+    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
+    if isinstance(_outv, str) and os.path.isfile(_outv):
+        shutil.move(_outv, _galaxy_outfile_name)
+        _galaxy_meta_data[_outn] = {'ext': '_sniff_'}
+    elif _numpy_available and isinstance(_outv, np.ndarray):
+        with open(_galaxy_outfile_name, 'wb') as fd:
+            np.savez(fd, _outv)
+        _galaxy_meta_data[_outn] = {'ext': 'npz'}
+    else:
+        with open(_galaxy_outfile_name, 'w') as fd:
+            json.dump(_outv, fd)
+        _galaxy_meta_data[_outn] = {'ext': 'expression.json'}
+
+with open(os.path.join(_galaxy_wd, 'galaxy.json'), 'w') as fd:
+    json.dump(_galaxy_meta_data, fd)
+print("*** Job finished successfully ***")
+