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from nugridpy import utils as u
from nugridpy import ascii_table as att
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
import numpy as np
from nugridpy import nugridse as mp
# MESA accretion
#run=mp.se('../mppnp/z2m2/m3z2m2/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z2m2/m3z2m2/kadon1/H5_restart','restart.h5')
#run=mp.se('../mppnp/z6m3/m15z6m3/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m15z6m3/ll22/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z6m3/m15z6m3/ne22a22/H5_restart','restart.h5')
#run3=mp.se('../mppnp/z6m3/m15z6m3/ne22a21/H5_restart','restart.h5')
#run=mp.se('../mppnp/z6m3/m15z6m3/newGe7023_noGe72pgGa72ng/H5_restart','restart.h5')
##run=mp.se('../mppnp/z2m2/m25z2m2/H5_restart','restart.h5')
##run1=mp.se('../mppnp/z2m2/m25z2m2/newGe703/H5_restart','restart.h5')
##run2=mp.se('../mppnp/z2m2/m25z2m2/newGe7023/H5_restart','restart.h5')
##run3=mp.se('../mppnp/z2m2/m25z2m2/newGe7023kad1/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m2z6m3/Ge7.02346/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m15z6m3/Ge75_mk2/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m2z6m3/Ges1.5us/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m2z6m3/Ge7.0346/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m2z6m3/Ge/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m2z6m3/Ge73_lower_mk3/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z6m3/m2z6m3/Ge73_upper_mk3/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m15z6m3/Ge73_lower_mk3/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z6m3/m15z6m3/Ge73_upper_mk3/H5_restart','restart.h5')
#run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m2z3m2/H5_out','out.h5')
#run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_noZ_iniabu_10i/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_4x10i/H5_out','out.h5')
##run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_0.5Mo96/H5_out','out.h5')
#run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m15z6m3_Reaclib0.5/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge70/frames/mppnp/RUN_set1upd_m15z6m3_Reaclib0.5_newGe70/H5_out','out.h5')
###run=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN_ll/frames/mppnp/RUN_set1upd_m25z6m3_Reaclib0.5_ll22/H5_out','out.h5')
###run1=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN_newNe22/frames/mppnp/RUN_set1upd_m25z6m3_Reaclib0.5_Ne22a22/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_nu/frames/mppnp/RUN_set1upd_m15z6m3_Reaclib0.5_ll22/H5_out','out.h5')
#run2=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_nu/frames/mppnp/RUN_set1upd_m15z6m3_Reaclib0.5_ne22a22/H5_out','out.h5')
#run=mp.se('../mppnp/z2m2/m3z2m2/critter/H5_out','out.h5')
#run1=mp.se('../mppnp/z1m2/m25z1m2/critter/H5_restart','restart.h5')
#run=mp.se('../mppnp/z6m3/m25z6m3/newGe703/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z1m2/m25z1m2/newGe703/H5_restart','restart.h5')
#run2=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge703/frames/mppnp/RUN_set1upd_m25z2m2_Reaclib0.5_newGe703/H5_out','out.h5')
#run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m2z1m2/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m2z2m2/H5_out','out.h5')
#run2=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m2z3m2/H5_out','out.h5')
#run= mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m2z3p5m2_hCBM_TDUx1p4_mk3/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z3p5m2_hCBM_TDUx1p4/H5_out','out.h5')
#run=mp.se('../mppnp/z6m3/m15z6m3/newGe7023_nosef/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z6m3/m25z6m3/newGe7023_nosef/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z1m2/m25z1m2/newGe7023_nosef/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z1m2/m2z1m2_he07/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z1m2/m3z1m2_he07/H5_restart','restart.h5')
#run1=mp.se('../mppnp/z2m2/m2z2m2_he07/H5_restart','restart.h5')
#run2=mp.se('../mppnp/z2m2/m3z2m2_he07/H5_restart','restart.h5')
#run=mp.se('../mppnp/z2m2/m3z2m2/noZ_iniabu/H5_restart','restart.h5') # noZ_iniabu
#run1=mp.se('../mppnp/z2m2/m3z2m2/noZ_iniabu_10i/H5_restart','restart.h5')
#run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_noZ_iniabu/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_noZ_iniabu_10i/H5_out','out.h5')
#run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2_noNe22+a/H5_out','out.h5')
#run=mp.se('../mppnp/z1m2/m25z1m2/H5_restart','restart.h5')
###run=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge703/frames/mppnp/RUN_set1upd_m15z6m3_Reaclib0.5_newGe703/H5_out','out.h5')
###run1=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge703/frames/mppnp/RUN_set1upd_m25z6m3_Reaclib0.5_newGe703/H5_out','out.h5')
###run2=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge703/frames/mppnp/RUN_set1upd_m25z1m2_Reaclib0.5_newGe703/H5_out','out.h5')
###run3=mp.se('/run/media/s1785107/Seagate Backup Plus Drive/NuclearPhysics/NuPPN_ge703/frames/mppnp/RUN_set1upd_m25z2m2_Reaclib0.5_newGe703/H5_out','out.h5')
#run1=mp.se('../mppnp/z1m2/m25z1m2/newGe7034/H5_restart','restart.h5')
#run=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/Chetec_Ne22_Umberto/m25z6m3_ne22ang_Longland/H5_out','out.h5')
#run1=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/Chetec_Ne22_Umberto/m25z6m3_ne22ang_stst_TAMU/H5_out','out.h5')
#run2=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/Chetec_Ne22_Umberto/m25z6m3_ne22ang_lowst_TAMU/H5_out','out.h5')
#run3=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/Chetec_Ne22_Umberto/m25z6m3_ne22ang_sthi_TAMU/H5_out','out.h5')
#run =mp.se('/home/ashley/Work/Yield_uncertainties/Pavel/H5_restart','restart.h5')
run=mp.se('/media/ashley/Seagate Backup Plus Drive/eddie3/NuclearPhysics/NuPPN/frames/mppnp/RUN_set1upd_m3z2m2/H5_out','out.h5')
ira = [run]#,run1]#,run2,run3]
ira_shift = [1,1,1,1,1,1,1,1,1,1,1,1]
ira_label_and_first_column = ['specie',#'M2.z3m2 mk2','M2.z3m2 mk1']
#'2M$\odot$','3M$\odot$']
#'m3z2m2','no TP']
#'M15.z6m3 ge70,73',
#'M25.z2m2','M25.z2m2 newGe703','M25.z2m2 newGe7023','M25.z2m2 newGe7023kad1']#,'M25.z2m2 ge70,73']
#'M15.z6m3 ge70,72,73 no 72Ge(p,g) or 72Ga(n,g)','M25.z6m3 ge70,72,73 no 72Ge(p,g) or 72Ga(n,g)','M25.z1m2 ge70,72,73 no 72Ge(p,g) or 72Ga(n,g)']
#'M15.z1m2 ge70,73','M15.z2m2 ge70,73']
#'M15.z1m2 Ge7203ntof','M15.z1m2 Ge7203ntof_lower','M15.z1m2 Ge7203ntof_upper',#]
#'M15.z1m2 Ge7203kad1','M15.z1m2 Ge7203kad1_lower','M15.z1m2 Ge7203kad1_upper']
#'M25.z1m2 newGe7023kad1','M25.z2m2 newGe7023kad1','M25.z6m3 newGe7023kad1']
#'M25.z1m2 ge70,73','M25.z1m2 ge70,73,74']
#'$M15.z6m3$ $Longland$','$M15.z6m3$ $This$ $work$']#,'$M15.z6m3$ $This$ $work$ $low$ $(\\alpha,\gamma)$']
#'M2.z6m3','M2.z6m3 new Ge73 macs lower','M2.z6m3 new Ge73 macs upper']
#'M15.z1m2','M15.z1m2 new Ge macs']
#'M2.z3p5m2','M3.z3p5m2']
#'M2.z1m2','M3.z1m2']
#'M3.z2m2 no Z','M3.z2m2 no Z 4x10i']
#'M3.z2m2','M3.z2m2 10i']
#'M25.z6m3 new Ge70,73 macs','M25.z1m2 new Ge70,73 macs','M25.z2m2 new Ge70,73 macs']
#'specie','M3.z2m2 KADoNiS 0.3','M3.z2m2 KADoNiS 1.0'] ## ACRETION
#'Longland', 'This work','This work low ($\\alpha$,n)','This work high ($\\alpha$,$\\gamma$)']
#'master']
'modular2']
form_str='%7.3E'
#headers=['this is a test','to make various type of tables']
headers=['Production factors','on accreting WD of different masses']
file_name_table_species_1='table_selected_isotopes_for_a_mass_coord.dat'
file_name_table_element_1='table_elements_for_a_mass_coord.dat'
sep_string=' & '
inc_fac=[1.,1.,1.,1.,1.,1.]
accretion=True
# specify here what do you want to plot
I_want_mass_fractions_plot = True
I_want_production_factors_plot = I_want_production_factors = False
I_want_only_stable = I_want_decayed = True
# some general input for the plots
# inputs to set
#mass_coord_I_want = [0.6868290554247601]*2 #m3z2m2 end surface
#mass_coord_I_want = [0.642276]*2 ##ACCRETION
#mass_coord_I_want = [2.6, 2.6, 2.6, 2.6, 2.6, 2.6] #MS m15 ##ACCRETION
#mass_coord_I_want = [3.355, 3.355, 3.355, 3.355] #MS m15z6m3 new##ACCRETION
#mass_coord_I_want = [7.4307, 7.4307, 7.4307, 7.4307] #MS m25z6m3 ##ACCRETION
#mass_coord_I_want = [7.231, 7.231, 7.231, 7.231] #MS m25z1m2 ##ACCRETION
#mass_coord_I_want = [3.23 ,3.23 ,3.23 ,3.23 ,3.23 ,3.23] #MS m15z1m2 ##ACCRETION
#mass_coord_I_want = [2.0]*6 #MS m15z1m2 ##ACCRETION 3.14,3.16, 3.18, 3.2, 3.21, 3.22
#mass_coord_I_want = [3.05 ,3.05 ,3.05 ,3.05] #MS m15z2m2 ##ACCRETION
#mass_coord_I_want = [6.947 ,6.947 ,6.947 ,6.947] #MS m25z2m2 ##ACCRETION
#mass_coord_I_want = [1.0, 0.68] #AGB z1m2_he07 ##ACCRETION
#mass_coord_I_want = [1.0, 0.75] #AGB z2m2_he07 ##ACCRETION
#mass_coord_I_want = [0.69, 0.71] #AGB z3m2 ##ACCRETION
#mass_coord_I_want = [4.6, 4.6, 5.4] #MS m25 ##ACCRETION
#mass_coord_I_want = [0.66,0.69,0.69] #AGB m2 ##ACCRETION
mass_coord_I_want = [6.2, 6.2, 6.2, 6.2] #MS m25z6m3 umberto ##ACCRETION
I_want_all = True
#I_want_decayed = True
#I_want_production_factors = False
mass=[]
j=0
for i in ira:
mass.append(i.se.get(i.se.cycles[len(i.se.cycles)-ira_shift[j]],'mass')) # i.se.cycles[len(i.se.cycles)-ira_shift[j]]
j=j+1
mass_coord_I_get=[]
zone_I_get=[]
for j in range(0,len(mass)):
for i in range(0,len(mass[j])):
if mass_coord_I_want[j] == mass[j][i]:
mass_coo_I_get.append(mass[j][i])
zone_I_get.append(int(i))
elif mass_coord_I_want[j] > mass[j][i]:
try:
dum = mass[j][i+1]
if mass_coord_I_want[j] <= mass[j][i+1]:
mass_coord_I_get.append(mass[j][i+1])
zone_I_get.append(int(i+1))
except IndexError:
mass_coord_I_get.append(mass[j][i])
zone_I_get.append(int(i))
# abundance are read here, for the cycle we selected
all_abundances = []
all_production_factors = []
j=0
if not I_want_decayed:
for i in ira:
all_abundances.append(i.se.get(i.se.cycles[len(i.se.cycles)-ira_shift[j]],'iso_massf')[zone_I_get[j]]) # i.se.cycles[len(i.se.cycles)-ira_shift[j]]
if I_want_production_factors:
i.get_abundance_iso_decay(i.se.cycles[len(i.se.cycles)-ira_shift[j]]) # i.se.cycles[len(i.se.cycles)-ira_shift[j]]
all_production_factors.append(i.se.cycles[len(i.se.cycles)-ira_shift[j]]) # i.se.cycles[len(i.se.cycles)-ira_shift[j]]
j=j+1
else:
for i in ira:
i.get_abundance_iso_decay(i.se.cycles[len(i.se.cycles)-ira_shift[j]]) # i.se.cycles[len(i.se.cycles)-ira_shift[j]]
all_abundances.append(np.array(i.decayed_stable_isotopes_per_cycle[zone_I_get[j]]))
if I_want_production_factors:
all_production_factors.append(i.isotopic_production_factors_decayed[zone_I_get[j]])
j=j+1
# isotopes I want to include in the table
if I_want_all:
isotopes_I_want = []
for i in ira:
isotopes_I_want.append(i.se.isotopes)
index_isotopes_I_want = []
j=0
for i in ira:
index_dum=[]
for iso_dum in isotopes_I_want[j]:
index_dum.append(i.se.isotopes.index(iso_dum))
index_isotopes_I_want.append(index_dum)
else:
isotopes_I_want = u.species_list("list_marco_1")
index_isotopes_I_want = []
for i in ira:
index_dum=[]
for iso_dum in isotopes_I_want:
index_dum.append(i.se.isotopes.index(iso_dum))
index_isotopes_I_want.append(index_dum)
# if I want decayed I need to convert naming scheme for isotopes_I_want
if I_want_decayed:
if I_want_all:
j=0
for i in ira:
u.convert_specie_naming_from_h5_to_ppn(isotopes_I_want[j])
isotopes_I_want[j] = u.spe
j=j+1
else:
u.convert_specie_naming_from_h5_to_ppn(isotopes_I_want)
isotopes_I_want = u.spe
####################################################
fig = plt.figure(1) # Figure object
ax = fig.add_subplot(1,1,1) # Axes object: one row, one column, first plot (one plot!)
# Tick marks
xminorlocator = plt.MultipleLocator(1)
xmajorlocator = plt.MultipleLocator(10)
ax.xaxis.set_major_locator(xmajorlocator)
ax.xaxis.set_minor_locator(xminorlocator)
yminorlocator = plt.MultipleLocator(0.1)
ymajorlocator = plt.MultipleLocator(1)
ax.yaxis.set_major_locator(ymajorlocator)
ax.yaxis.set_minor_locator(yminorlocator)
plt.ylabel('Mass Fraction (X)', fontsize=40)
plt.xlabel('A', fontsize=40)
ax.xaxis.get_majorticklocs()
plt.rcParams['text.usetex'] = True
plt.rcParams['axes.linewidth'] = 2
plt.rcParams['xtick.major.size'] = 20
plt.rcParams['xtick.major.width'] = 2
plt.rcParams['xtick.minor.size'] = 10
plt.rcParams['xtick.minor.width'] = 2
plt.rcParams['ytick.major.size'] = 20
plt.rcParams['ytick.major.width'] = 2
plt.rcParams['ytick.minor.size'] = 10
plt.rcParams['ytick.minor.width'] = 2
plt.rcParams['xtick.labelsize'] = 30
plt.rcParams['ytick.labelsize'] = 30
plt.tick_params(axis='both',which='both',pad=4,direction='in')
#plt.show()
###################################################################
fig = plt.figure(2) # Figure object
ax = fig.add_subplot(1,1,1) # Axes object: one row, one column, first plot (one plot!)
# Tick marks
xminorlocator = plt.MultipleLocator(1)
xmajorlocator = plt.MultipleLocator(10)
ax.xaxis.set_major_locator(xmajorlocator)
ax.xaxis.set_minor_locator(xminorlocator)
yminorlocator = plt.MultipleLocator(0.1)
ymajorlocator = plt.MultipleLocator(1)
ax.yaxis.set_major_locator(ymajorlocator)
ax.yaxis.set_minor_locator(yminorlocator)
plt.ylabel('Mass Fraction (X)', fontsize=40)
plt.xlabel('A', fontsize=40)
ax.set_yscale('log')
symbols=["b:s", "r--o", "g-+", "y-D",'r-^']
size=25
if I_want_production_factors_plot:
symbols=["gs", "rD", "bd", "yo",'k^','m*','cv',"go", "rD", "kH", "yh"]
color_plot=['g','r','b','y','k','m','c','g','r','k','y']
line_style=[':','--','-','-.',':','--','-','-.',':','--','-']
if I_want_only_stable:
j=0
for i in ira:
k=0
if j < (len(ira)):
if accretion:
for jj in range(len(i.stable_isotope_list)):
if jj==0:
if (i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]] > 85):
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_production_factors[j][jj]*inc_fac[j],symbols[j],label=ira_label_and_first_column[j+1],markersize=15.)
else:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_production_factors[j][jj],symbols[j],label=ira_label_and_first_column[j+1],markersize=15.)
else:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_production_factors[j][jj]*inc_fac[j],symbols[j],markersize=15.)
k=k+1
else:
for jj in range(len(i.stable_isotope_list)):
if jj==0:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_production_factors[j][jj],symbols[j],label=ira_label_and_first_column[j+1],markersize=15.)
else:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_production_factors[j][jj],symbols[j],markersize=15.)
k=k+1
j=j+1
plt.xticks(size=size)
plt.yticks(size=size)
j=0
for i in ira:
if j < (len(ira)):
for ii in range(len(i.stable_isotope_list)):
for jj in range(len(i.stable_isotope_list)):
if i.stable_isotope_list[ii][:2] == i.stable_isotope_list[jj][:2]:
if i.stable_isotope_list[ii] == i.stable_isotope_list[jj-1]:
adum=[i.se.A[i.index_for_all_species[i.stable_isotope_list[ii].capitalize()]],i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]]]
#print(adum,'adum')
if accretion:
mfdum =[float(all_production_factors[j][i.index_for_stable_species[i.stable_isotope_list[ii].upper()]]*inc_fac[j]),float(all_production_factors[j][i.index_for_stable_species[i.stable_isotope_list[jj].upper()]]*inc_fac[j])]
else:
mfdum =[float(all_production_factors[j][i.index_for_stable_species[i.stable_isotope_list[ii].upper()]]),float(all_production_factors[j][i.index_for_stable_species[i.stable_isotope_list[jj].upper()]])]
#print(mfdum,'mfdum')
plt.plot(adum,mfdum,'k-')
j=j+1
plt.xlabel('$Mass$ $number$', fontsize=40)
plt.ylabel('$X_{i}/X_{\odot}$', fontsize=40)
#plt.ylabel('$Production$ $factor$', fontsize=30)
plt.ylim(0.,100.)
plt.xlim(55,210) ## ACCRETION
plt.legend(numpoints=1,loc='best',prop={'size':25})
plt.gcf().subplots_adjust(bottom=0.15)
if I_want_mass_fractions_plot:
symbols=["gs", "rD", "bd", "yo",'k^','m*','cv',"go", "rD", "kH", "yh"]
if I_want_only_stable:
j=0
for i in ira: ##### MY MODIFICATION.....
k=0
if j < (len(ira)):
for jj in range(len(i.stable_isotope_list)):
if jj==0:
if (i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]] > 85):
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_abundances[j][jj]*inc_fac[j],symbols[j],label=ira_label_and_first_column[j+1],markersize=15.)
else:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_abundances[j][jj],symbols[j],label=ira_label_and_first_column[j+1],markersize=15.)
else:
plt.plot(i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]],all_abundances[j][jj]*inc_fac[j],symbols[j],markersize=15.)
k=k+1
j=j+1
j=0
for i in ira:
if j < (len(ira)):
for ii in range(len(i.stable_isotope_list)):
for jj in range(len(i.stable_isotope_list)):
if i.stable_isotope_list[ii][:2] == i.stable_isotope_list[jj][:2]:
if i.stable_isotope_list[ii] == i.stable_isotope_list[jj-1]:
adum=[i.se.A[i.index_for_all_species[i.stable_isotope_list[ii].capitalize()]],i.se.A[i.index_for_all_species[i.stable_isotope_list[jj].capitalize()]]]
#print(adum,'adum')
if accretion:
mfdum =[float(all_abundances[j][i.index_for_stable_species[i.stable_isotope_list[ii].upper()]]*inc_fac[j]),float(all_abundances[j][i.index_for_stable_species[i.stable_isotope_list[jj].upper()]]*inc_fac[j])]
else:
mfdum =[float(all_abundances[j][i.index_for_stable_species[i.stable_isotope_list[ii].upper()]]),float(all_abundances[j][i.index_for_stable_species[i.stable_isotope_list[jj].upper()]])]
#print(mfdum,'mfdum')
plt.plot(adum,mfdum,'k-')
j=j+1
plt.ylim(1.0e-4,5.)
plt.xlim(55,211)
plt.legend(numpoints=1,loc='best',prop={'size':30})
plt.show()
# make data table
# not yet implemented production factors in isotopic table.
if I_want_production_factors:
all_abund_table = all_production_factors
else:
all_abund_table = all_abundances
#arguments for isotopic table:
data=[]
j=0
if not I_want_decayed:
for i in ira:
data.append(all_abundances[j][index_isotopes_I_want[j]])
j=j+1
if I_want_all:
species_for_table=[]
species_for_table=isotopes_I_want
else:
if I_want_all:
species_for_table=[]
for i in ira:
data_dum = []
species_dum=[]
for k in range(0,len(isotopes_I_want[j])):
try:
if (k > 277): ## MY MODIF
data_dum.append(all_abund_table[j][i.index_for_stable_species[isotopes_I_want[j][k].upper()]]*inc_fac[j]) ## HERE ABUNDANCES ARE READ
species_dum.append(isotopes_I_want[j][k].upper())
else:
data_dum.append(all_abund_table[j][i.index_for_stable_species[isotopes_I_want[j][k].upper()]]) ## HERE ABUNDANCES ARE READ
species_dum.append(isotopes_I_want[j][k].upper())
except KeyError:
print('I am not stable',isotopes_I_want[j][k].upper(), 'k= ', k)
species_for_table.append(species_dum)
data.append(data_dum)
j=j+1
if False:
data_dum = []
species_dum=[]
for k in range(0,len(isotopes_I_want[j-1])):
try:
if all_abund_table[j-1][i.index_for_stable_species[isotopes_I_want[j-1][k].upper()]] > min_prod_fac :
data_dum.append(all_abund_table[j-1][i.index_for_stable_species[isotopes_I_want[j-1][k].upper()]]*(all_abund_table[j-1][i.index_for_stable_species[isotopes_I_want[j-1][k].upper()]]/all_abund_table[j-2][i.index_for_stable_species[isotopes_I_want[j-2][k].upper()]]))
species_dum.append(isotopes_I_want[j-1][k].upper())
else:
data_dum.append(all_abund_table[j-1][i.index_for_stable_species[isotopes_I_want[j-1][k].upper()]])
except KeyError:
print('I am not stable',isotopes_I_want[j-1][k].upper())
species_for_table.append(species_dum)
data.append(data_dum)
else:
for i in ira:
data_dum = []
for k in range(0,len(isotopes_I_want)):
data_dum.append(all_abund_table[j][i.index_for_stable_species[isotopes_I_want[k].upper()]])
data.append(data_dum)
j=j+1
# combine data with first string column into one list
# now on, I am assuming that the distribution has the species in the same order,
# or the same network. This cannot be true! Careful. Marco
if I_want_all:
isotopes_I_want = species_for_table[0]
all_data=[]
#if I_want_neutron_exposure:
# isotopes_I_want.append(r'$\tau$(30 keV)')
# data=np.append(np.array(data),np.array(neutron_exposure).reshape(len(neutron_exposure),1),axis=1)
all_data.append(isotopes_I_want)
for i in range(len(data)):
datal=list(form_str%data[i][j] for j in range(len(data[i])))
all_data.append(datal)
### attempt to add the trailing '\\' to a latex table
final_col=len(isotopes_I_want)*[r'\\ ']
ira_label_and_first_column.append(r'\\ ')
all_data.append(final_col)
att.write(file_name_table_species_1,headers,ira_label_and_first_column,all_data,sep=sep_string)