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photoionization_lib.py
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-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Jun 30 09:54:20 2020
-Library of the photoionization model
-
-@author: sacha.foschino@hotmail.fr
-"""
-import matplotlib.pyplot as plt
-import numpy as np
-from astropy.table import Table
-
-def preparation_Fe(d,Av,wave_range,quiet):
-    '''Function adapting the radiation field (RF) to its use by the PE model
-    d: float, distance between the region modeled and the UV source, in cm, e.g. 4.413e+17cm for the 0.143pc separating HD200775 and the PDR front,
-    Av: float, Extinction in the V band, in mag,
-    wave_range: list of 2 elements, limits of the wavelength interval considered in nm, e.g. [91.16,2000],
-    quiet: bool, if False, plot the RF at each step of the conversion
-    
-    returns Fe_E_,E,Fe_l,wave ; i.e. respectively the RF in erg/sec/cm2/eV/sr, the photon energy vector, 
-            the RF in erg/sec/cm2/nm/sr and the corresponding wavelength vector
-    '''
-    # =============================================================================
-    # preparation of HD200775 radiation field: dillution + extinction
-    '''radiation field on HD200775'''
-#    wave_rad,spec_rad=np.loadtxt(rf_name,unpack=True,skiprows=4) #if another RF than that of HD200775 is used (e.g. Draine, Habing or Mathis)
-    wave_rad, spec_rad=np.loadtxt('./radiation_fields/HD200775_RF.txt', unpack=True)
-     
-    if not(quiet):
-        plt.figure(1)
-        plt.loglog(wave_rad,spec_rad,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-        plt.title('virgin spectrum')
-        plt.xlabel('wavelength (nm)')
-        plt.ylabel('Specific intensity (erg/sec/cm$^2$/nm/sr)')
-        plt.subplots_adjust(top=0.986,bottom=0.111,left=0.126,right=0.991,hspace=0.2,wspace=0.2)
-        plt.legend()
-        plt.tight_layout()
-
-    
-    '''wavelengths ranges for the G0 energies''' 
-    #selection of the wavelength range
-    spec7023=spec_rad[np.where((wave_rad>wave_range[0]) & (wave_rad<wave_range[1]))[0]]
-    wave=wave_rad[np.where((wave_rad>wave_range[0]) & (wave_rad<wave_range[1]))[0]]
-
-    #intensity of HD200775
-    if not(quiet):
-        plt.figure(2)
-        plt.loglog(wave,spec7023,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-        plt.title('virgin spectrum cut')
-        plt.xlabel('wavelength (nm)')
-        plt.ylabel('Specific intensity (erg/sec/cm$^2$/nm/sr)')
-        plt.subplots_adjust(top=0.986,bottom=0.111,left=0.126,right=0.991,hspace=0.2,wspace=0.2)
-        plt.legend()
-        plt.tight_layout()
-
-
-    '''interpolation of the extinction coefficients with HD200775's RF wavelength vector'''
-    wave_draine__, albe, cos, cext__ = np.loadtxt('./extinction_curves/draine_curve_55.txt', unpack=True, usecols=[0,1,2,3], skiprows=80) 
-    Cext=np.interp(wave,wave_draine__[::-1]*1e3,cext__[::-1]) #/!\ reverse the order of the cext__ vector
-    
-    '''geometrical dillution'''
-    R=10*70000000000 #radius of the star in cm, Pilleri et al. 2012
- #   d=0.143*3.086e18
-    intensity_diluted=spec7023*(R/d)**2
-    
-    if not(quiet):
-        plt.figure(3)
-        plt.loglog(wave,intensity_diluted,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-        plt.title('diluted spectrum')
-        plt.xlabel('wavelength (nm)')
-        plt.ylabel('Specific intensity (erg/sec/cm$^2$/nm/sr)')
-        plt.subplots_adjust(top=0.986,bottom=0.111,left=0.126,right=0.991,hspace=0.2,wspace=0.2)
-        plt.legend()
-        plt.tight_layout()
-    
-    '''extinction'''
-    NH=2e21 #conlumn density in cm-2, a column density of 2e21cm-2 implies an Av of 1mag
-#    Av=0
-    taunu=NH*Av*Cext #opacity    
-    Fe_l=intensity_diluted*np.exp(-taunu) #intensity diluted and extincted
-    if not(quiet):
-        plt.figure(4)
-        plt.loglog(wave,Fe_l,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-        plt.title('ext spectrum')
-        plt.xlabel('wavelength (nm)')
-        plt.ylabel('Specific intensity (erg/sec/cm$^2$/nm/sr)')
-        plt.legend()
-        plt.tight_layout()
-    
-    
-
-    '''conversion in erg/sec/cm2/sr/eV'''
-    c=299792458000000000 #light speed in nm
-    h=4.135667516e-15 #planck constant in eV*sec
-    
-    E=(h*c/wave)[::-1] #ev
-    Fe_E_=Fe_l[::-1]*h*c/(E**2)
-    
-    if not(quiet):
-        plt.figure(5)
-        plt.loglog(E,Fe_E_,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-#        plt.loglog(E,Fe_E_,label='d={:.0f}mpc, {:.0f}" '.format(d/3.086e15,d/(3.086e18*3.4268e-3)))
-        plt.title('energy spectrum')
-        plt.xlabel('photon energy (eV)')
-        plt.ylabel('Specific intensity (erg/sec/cm$^2$/eV/sr)')
-        plt.subplots_adjust(top=0.986,bottom=0.111,left=0.126,right=0.991,hspace=0.2,wspace=0.2)
-        plt.legend()
-        plt.tight_layout()
-
-    return Fe_E_,E,Fe_l,wave
-
-
-    
-    
-def yield_n_to_p(E,IP):
-    from numpy import where, concatenate,zeros,full
-    '''adapt the photoelectric yield Neutral -> Cation
-    version from Joachims et al 1996
-    E: 1xn array, photonenergy vector
-    IP: float, first ionization potential of the molecule
-    
-    returns the yield of the first photoionization
-    '''
-
-    first_part=where(E<IP)[0]
-    scdn_part=where((E>=IP) & (E<(IP+9.2)))[0]
-    third_part=where((E>IP+9.2))[0]
-    
-    Y_1=zeros([len(first_part)])
-    Y_2=(E[scdn_part]-IP)/9.2
-    Y_3=full(len(third_part), 1)
-
-    Yntop=concatenate((Y_1,Y_2,Y_3))
-    return Yntop    
-
-
-def yield_p_to_2p(E,IP2,Nc,alpha=0.3):
-    from numpy import where, concatenate,zeros,full
-    '''adapt the photoelectric yield Cation -> Dication to the molecule
-    version from Wenzel et al 2020
-    E: 1xn array, photonenergy vector
-    IP2: float, second ionization potential of the molecule
-    Nc: int or float, size of the PAH in number of carbon atoms 
-    alpha: steepness coefficient, see Wenzel et al. 2020, this parameter should not change
-    
-    returns the yield of the second photoionization
-    '''
-    
-    if (Nc>=32) & (Nc<50):
-        beta=0.59+8.1e-3*Nc
-    if Nc>=50:
-        beta=1
-
-    first_part=where(E<IP2)[0]
-    scdn_part=where((E>=IP2) & (E<(11.3)))[0]
-    third_part=where((E>=11.3) & (E<(12.9)))[0]
-    fourth_part=where((E>=12.9) & (E<(13.6)))[0]
-#    print(Nc)
-    Y_1=zeros([len(first_part)])
-    Y_2=alpha/(11.3-IP2)*(E[scdn_part]-IP2)
-    Y_3=full(len(third_part), alpha)
-    Y_4=(beta-alpha)/2.1*(E[fourth_part]-12.9)+alpha
-    Yptopp=concatenate((Y_1,Y_2,Y_3,Y_4))
-    
-    return Yptopp
-    
-def IP_estimate(Nc,Z):
-    '''gives the estimate of the IP from Z to Z+1 according to Eq.1 of Wenzel et al. 2020
-    Nc: int of float, size of the PAH in carbon atoms
-    Z: positive int, the charge state of the molecule 
-    
-    returns the IP of the molecule'''
-    
-    eps0=8.85e-21 #en F/nm
-    e=1.6e-19 #en C
-    
-    IP=3.9+(1/(4*np.pi*eps0))*((Z+0.5)*(e**2)/((Nc/468)**(1/3))+(Z+2)*((e**2)/((Nc/468)**(1/3)))*0.03/((Nc/468)**(1/3)))*1/e #en eV
-    
-    return IP
-
-
-
-
-def cross_secs(Nc,quiet):
-    '''==========================|building of the cross section|======================='''
-    ''' derives a mean photoabsorption cross section of the molecule considered, in 3 size ranges 
-    Nc: int, size of the molecule in carbon atoms
-    quiet: bool, if False plot the resulting cross sections'''
-    #absorption cross section
-    if (Nc>=32) & (Nc<40):
-        #32 a 40
-        eVN_,crossN_1_1=np.loadtxt('./neutrals/ovalene_neutral.txt',unpack=True) #C32
-        eVC_,crossC_1_1=np.loadtxt('./cations/ovalene_cation.txt',unpack=True) #C32
-        eVDC_,crossDC_1_1=np.loadtxt('./dications/ovalene_dication.txt',unpack=True) #C32
-        
-        eVN_,crossN_2_1=np.loadtxt('./neutrals/tetrabenzocoronene_neutral.txt',unpack=True) #C36
-        eVC_,crossC_2_1=np.loadtxt('./cations/tetrabenzocoronene_cation.txt',unpack=True) #C36
-        eVDC_,crossDC_2_1=np.loadtxt('./dications/tetrabenzocoronene_dication.txt',unpack=True) #C36
-        
-        eVN_,crossN_3_1=np.loadtxt('./neutrals/circumbiphenyl_neutral.txt',unpack=True) #C38
-        eVC_,crossC_3_1=np.loadtxt('./cations/circumbiphenyl_cation.txt',unpack=True) #C38
-        eVDC_,crossDC_3_1=np.loadtxt('./dications/circumbiphenyl_dication.txt',unpack=True) #C38
-        
-        cross_N_=(((crossN_1_1/32)+(crossN_2_1/36)+(crossN_3_1/38))/3)*Nc
-        cross_C_=(((crossC_1_1/32)+(crossC_2_1/36)+(crossC_3_1/38))/3)*Nc
-        cross_DC_=(((crossDC_1_1/32)+(crossDC_2_1/36)+(crossDC_3_1/38))/3)*Nc
-        
-        E_range=np.where(eVN_<13.6)[0]
-        
-        if not(quiet):
-            plt.figure(121)
-            plt.plot(eVN_[E_range],cross_N_[E_range],'b',label='Z=0')
-            plt.plot(eVC_[E_range],cross_C_[E_range],'r',label='Z=1')
-            plt.plot(eVDC_[E_range],cross_DC_[E_range],'orange',label='Z=2')
-            plt.ylabel('$\sigma$ (Mb)')
-            plt.xlabel('photon energy (eV)')
-            plt.legend()
-#        plt.plot(eVN_[E_range],crossN_1_1[E_range])
-#        plt.plot(eVN_[E_range],crossN_2_1[E_range])
-#        plt.plot(eVN_[E_range],crossN_3_1[E_range])
-    elif (Nc>=40) & (Nc<48):
-        #40 a 48
-
-        eVN_,crossN_1_2=np.loadtxt('./neutrals/circumanthracene_neutral.txt',unpack=True) #C40
-        eVC_,crossC_1_2=np.loadtxt('./cations/circumanthracene_cation.txt',unpack=True) #C40
-        eVDC_,crossDC_1_2=np.loadtxt('./dications/circumanthracene_dication.txt',unpack=True) #C40
-        
-        eVN_,crossN_2_2=np.loadtxt('./neutrals/circumpyrene_neutral.txt',unpack=True) #C42
-        eVC_,crossC_2_2=np.loadtxt('./cations/circumpyrene_cation.txt',unpack=True) #C42
-        eVDC_,crossDC_2_2=np.loadtxt('./dications/circumpyrene_dication.txt',unpack=True) #C42
-        
-        eVN_,crossN_3_2=np.loadtxt('./neutrals/hexabenzocoronene_neutral.txt',unpack=True) #C42
-        eVC_,crossC_3_2=np.loadtxt('./cations/hexabenzocoronene_cation.txt',unpack=True) #C42
-        eVDC_,crossDC_3_2=np.loadtxt('./dications/hexabenzocoronene_dication.txt',unpack=True) #C42    
-
-        E_range=np.where(eVN_<13.6)[0]
-        
-        cross_N_=(((crossN_1_2/40)+(crossN_2_2/42)+(crossN_3_2/42))/3)*Nc
-        cross_C_=(((crossC_1_2/40)+(crossC_2_2/42)+(crossC_3_2/42))/3)*Nc
-        cross_DC_=(((crossDC_1_2/40)+(crossDC_2_2/42)+(crossDC_3_2/42))/3)*Nc
-        if not(quiet):
-        
-            plt.figure(121)
-            plt.plot(eVN_[E_range],cross_N_[E_range],'b',label='Z=0')
-            plt.plot(eVC_[E_range],cross_C_[E_range],'r',label='Z=1')
-            plt.plot(eVDC_[E_range],cross_DC_[E_range],'orange',label='Z=2')
-            plt.ylabel('$\sigma$ (Mb)')
-            plt.xlabel('photon energy (eV)')
-            plt.legend()
-#        plt.plot(eVN_[E_range],crossN_1_1[E_range])
-#        plt.plot(eVN_[E_range],crossN_2_1[E_range])
-#        plt.plot(eVN_[E_range],crossN_3_1[E_range])
-    elif (Nc>=48):
-        #48 a 66
-        eVN_,crossN_1_3=np.loadtxt('./neutrals/dicoronylene_neutral.txt',unpack=True) #C48
-        eVC_,crossC_1_3=np.loadtxt('./cations/dicoronylene_cation.txt',unpack=True) #C48
-        eVDC_,crossDC_1_3=np.loadtxt('./dications/dicoronylene_dication.txt',unpack=True) #C48
-        
-        eVN_,crossN_2_3=np.loadtxt('./neutrals/circumcoronene_neutral.txt',unpack=True) #C54
-        eVC_,crossC_2_3=np.loadtxt('./cations/circumcoronene_cation.txt',unpack=True) #C54
-        eVDC_,crossDC_2_3=np.loadtxt('./dications/circumcoronene_dication.txt',unpack=True) #C54
-        
-        eVN_,crossN_3_3=np.loadtxt('./neutrals/circumovalene_neutral.txt',unpack=True) #C66
-        eVC_,crossC_3_3=np.loadtxt('./cations/circumovalene_cation.txt',unpack=True) #C66
-        eVDC_,crossDC_3_3=np.loadtxt('./dications/circumovalene_dication.txt',unpack=True) #C66
-        
-        E_range=np.where(eVN_<13.6)[0]
-        
-        cross_N_=(((crossN_1_3/48)+(crossN_2_3/54)+(crossN_3_3/66))/3)*Nc
-        cross_C_=(((crossC_1_3/48)+(crossC_2_3/54)+(crossC_3_3/66))/3)*Nc
-        cross_DC_=(((crossDC_1_3/48)+(crossDC_2_3/54)+(crossDC_3_3/66))/3)*Nc
-        if not(quiet):
-            plt.figure(121)
-            plt.plot(eVN_[E_range],cross_N_[E_range],'b',label='Z=0')
-            plt.plot(eVC_[E_range],cross_C_[E_range],'r',label='Z=1')
-            plt.plot(eVDC_[E_range],cross_DC_[E_range],'orange',label='Z=2')
-            plt.ylabel('$\sigma$ (Mb)')
-            plt.xlabel('photon energy (eV)')
-            plt.legend()
-    return eVN_[E_range],eVC_[E_range],eVDC_[E_range],cross_N_[E_range],cross_C_[E_range],cross_DC_[E_range]
-                
-  
-    
-    
-    
-    
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