docs: def convert_specie_naming_from_h5_to_ppn(isotope_names):
      '''
      read isotopes names from h5 files, and convert them
      according to standard scheme used inside ppn and mppnp.  Also
      Z and A are recalculated, for these species. Isomers are
      excluded for now, since there were recent changes in isomers
      name. As soon as the isomers names are settled, than Z and A
      provided here will be obsolete, and can be changed by usual Z
      and A.
  
      '''
  
      spe_rude1 = []
      spe_rude2 = []
      spe_rude3 = []
      for i in range(len(isotope_names)):
          spe_rude1.append(isotope_names[i].split('-')[0])
          spe_rude2.append(isotope_names[i].split('-')[1])
      # spe_rude1 is elem name and spe_rude2 is mass number.
      #print spe_rude1,spe_rude2
      k = 0
      for i in range(len(spe_rude1)):
          try:
              if int(spe_rude2[i]) < 10:
                  spe_rude3.append(str(spe_rude1[i][0:2])+str('  ')+str(spe_rude2[i][0:3]))
              elif int(spe_rude2[i]) >= 10 and int(spe_rude2[i]) < 100 :
                  spe_rude3.append(str(spe_rude1[i][0:2])+str(' ')+str(spe_rude2[i][0:3]))
              elif int(spe_rude2[i]) >= 100 :
                  spe_rude3.append(str(spe_rude1[i][0:2])+str(spe_rude2[i][0:3]))
          except ValueError:
              k = k+1
              None
  
      global spe
      spe = []
      global n_array
      n_array = []
      for i in range(len(spe_rude3)):
          if len(str(spe_rude1[i])) == 1:
              spe.append(str(spe_rude3[i][0:1])+str(' ')+str(spe_rude3[i][1:4]))
          else:
              spe.append(spe_rude3[i])
          n_array.append(i)
      if spe[0]=='Ne  1':
          spe[0] = 'N   1'
  
      # spe_rude is the isotope name, in agreement with what we use in ppn, etc.
      # need to do this to can use other functions without changing them drastically.
  
  
  
      # here I skip isomers...
      global amass_int
      amass_int=np.zeros(len(spe_rude2))
      for i in range(len(spe_rude2)-k):
          amass_int[i]=int(spe_rude2[i])
          #print amass_int
  
  
      # here I have to create an array for the atomic numbers.
      # I need to this when I calculate and plot element abundances
  
      global znum_int
      znum_int=np.zeros(len(spe))
  
      for i in range(len(spe)):
          znum_int[i] = Utils.elements_names.index(str(spe[i][0:2]).strip())
          # changed by alex
          # if str(spe[i][0:2]) == 'H ':
          #     znum_int[i] = 1
          # elif str(spe[i][0:2]) == 'He':
          #     znum_int[i] = 2
          # elif str(spe[i][0:2]) == 'Li':
          #     znum_int[i] = 3
          # elif str(spe[i][0:2]) == 'Be':
          #     znum_int[i] = 4
          # elif str(spe[i][0:2]) == 'B ':
          #     znum_int[i] = 5
          # elif str(spe[i][0:2]) == 'C ':
          #     znum_int[i] = 6
          # elif str(spe[i][0:2]) == 'N ':
          #     znum_int[i] = 7
          # elif str(spe[i][0:2]) == 'O ':
          #     znum_int[i] = 8
          # elif str(spe[i][0:2]) == 'F ':
          #     znum_int[i] = 9
          # elif str(spe[i][0:2]) == 'Ne':
          #     znum_int[i] = 10
          # elif str(spe[i][0:2]) == 'Na':
          #     znum_int[i] = 11
          # elif str(spe[i][0:2]) == 'Mg':
          #     znum_int[i] = 12
          # elif str(spe[i][0:2]) == 'Al':
          #     znum_int[i] = 13
          # elif str(spe[i][0:2]) == 'Si':
          #     znum_int[i] = 14
          # elif str(spe[i][0:2]) == 'P ':
          #     znum_int[i] = 15
          # elif str(spe[i][0:2]) == 'S ':
          #     znum_int[i] = 16
          # elif str(spe[i][0:2]) == 'Cl':
          #     znum_int[i] = 17
          # elif str(spe[i][0:2]) == 'Ar':
          #     znum_int[i] = 18
          # elif str(spe[i][0:2]) == 'K ':
          #     znum_int[i] = 19
          # elif str(spe[i][0:2]) == 'Ca':
          #     znum_int[i] = 20
          # elif str(spe[i][0:2]) == 'Sc':
          #     znum_int[i] = 21
          # elif str(spe[i][0:2]) == 'Ti':
          #     znum_int[i] = 22
          # elif str(spe[i][0:2]) == 'V ':
          #     znum_int[i] = 23
          # elif str(spe[i][0:2]) == 'Cr':
          #     znum_int[i] = 24
          # elif str(spe[i][0:2]) == 'Mn':
          #     znum_int[i] = 25
          # elif str(spe[i][0:2]) == 'Fe':
          #     znum_int[i] = 26
          # elif str(spe[i][0:2]) == 'Co':
          #     znum_int[i] = 27
          # elif str(spe[i][0:2]) == 'Ni':
          #     znum_int[i] = 28
          # elif str(spe[i][0:2]) == 'Cu':
          #     znum_int[i] = 29
          # elif str(spe[i][0:2]) == 'Zn':
          #     znum_int[i] = 30
          # elif str(spe[i][0:2]) == 'Ga':
          #     znum_int[i] = 31
          # elif str(spe[i][0:2]) == 'Ge':
          #     znum_int[i] = 32
          # elif str(spe[i][0:2]) == 'As':
          #     znum_int[i] = 33
          # elif str(spe[i][0:2]) == 'Se':
          #     znum_int[i] = 34
          # elif str(spe[i][0:2]) == 'Br':
          #     znum_int[i] = 35
          # elif str(spe[i][0:2]) == 'Kr':
          #     znum_int[i] = 36
          # elif str(spe[i][0:2]) == 'Rb':
          #     znum_int[i] = 37
          # elif str(spe[i][0:2]) == 'Sr':
          #     znum_int[i] = 38
          # elif str(spe[i][0:2]) == 'Y ':
          #     znum_int[i] = 39
          # elif str(spe[i][0:2]) == 'Zr':
          #     znum_int[i] = 40
          # elif str(spe[i][0:2]) == 'Nb':
          #     znum_int[i] = 41
          # elif str(spe[i][0:2]) == 'Mo':
          #     znum_int[i] = 42
          # elif str(spe[i][0:2]) == 'Tc':
          #     znum_int[i] = 43
          # elif str(spe[i][0:2]) == 'Ru':
          #     znum_int[i] = 44
          # elif str(spe[i][0:2]) == 'Rh':
          #     znum_int[i] = 45
          # elif str(spe[i][0:2]) == 'Pd':
          #     znum_int[i] = 46
          # elif str(spe[i][0:2]) == 'Ag':
          #     znum_int[i] = 47
          # elif str(spe[i][0:2]) == 'Cd':
          #     znum_int[i] = 48
          # elif str(spe[i][0:2]) == 'In':
          #     znum_int[i] = 49
          # elif str(spe[i][0:2]) == 'Sn':
          #     znum_int[i] = 50
          # elif str(spe[i][0:2]) == 'Sb':
          #     znum_int[i] = 51
          # elif str(spe[i][0:2]) == 'Te':
          #     znum_int[i] = 52
          # elif str(spe[i][0:2]) == 'I ':
          #     znum_int[i] = 53
          # elif str(spe[i][0:2]) == 'Xe':
          #     znum_int[i] = 54
          # elif str(spe[i][0:2]) == 'Cs':
          #     znum_int[i] = 55
          # elif str(spe[i][0:2]) == 'Ba':
          #     znum_int[i] = 56
          # elif str(spe[i][0:2]) == 'La':
          #     znum_int[i] = 57
          # elif str(spe[i][0:2]) == 'Ce':
          #     znum_int[i] = 58
          # elif str(spe[i][0:2]) == 'Pr':
          #     znum_int[i] = 59
          # elif str(spe[i][0:2]) == 'Nd':
          #     znum_int[i] = 60
          # elif str(spe[i][0:2]) == 'Pm':
          #     znum_int[i] = 61
          # elif str(spe[i][0:2]) == 'Sm':
          #     znum_int[i] = 62
          # elif str(spe[i][0:2]) == 'Eu':
          #     znum_int[i] = 63
          # elif str(spe[i][0:2]) == 'Gd':
          #     znum_int[i] = 64
          # elif str(spe[i][0:2]) == 'Tb':
          #     znum_int[i] = 65
          # elif str(spe[i][0:2]) == 'Dy':
          #     znum_int[i] = 66
          # elif str(spe[i][0:2]) == 'Ho':
          #     znum_int[i] = 67
          # elif str(spe[i][0:2]) == 'Er':
          #     znum_int[i] = 68
          # elif str(spe[i][0:2]) == 'Tm':
          #     znum_int[i] = 69
          # elif str(spe[i][0:2]) == 'Yb':
          #     znum_int[i] = 70
          # elif str(spe[i][0:2]) == 'Lu':
          #     znum_int[i] = 71
          # elif str(spe[i][0:2]) == 'Hf':
          #     znum_int[i] = 72
          # elif str(spe[i][0:2]) == 'Ta':
          #     znum_int[i] = 73
          # elif str(spe[i][0:2]) == 'W ':
          #     znum_int[i] = 74
          # elif str(spe[i][0:2]) == 'Re':
          #     znum_int[i] = 75
          # elif str(spe[i][0:2]) == 'Os':
          #     znum_int[i] = 76
          # elif str(spe[i][0:2]) == 'Ir':
          #     znum_int[i] = 77
          # elif str(spe[i][0:2]) == 'Pt':
          #     znum_int[i] = 78
          # elif str(spe[i][0:2]) == 'Au':
          #     znum_int[i] = 79
          # elif str(spe[i][0:2]) == 'Hg':
          #     znum_int[i] = 80
          # elif str(spe[i][0:2]) == 'Tl':
          #     znum_int[i] = 81
          # elif str(spe[i][0:2]) == 'Pb':
          #     znum_int[i] = 82
          # elif str(spe[i][0:2]) == 'Bi':
          #     znum_int[i] = 83
          # elif str(spe[i][0:2]) == 'Po':
          #     znum_int[i] = 84
          # elif str(spe[i][0:2]) == 'At':
          #     znum_int[i] = 85
          # elif str(spe[i][0:2]) == 'Rn':
          #     znum_int[i] = 86
          # elif str(spe[i][0:2]) == 'Fr':
          #     znum_int[i] = 87
          # elif str(spe[i][0:2]) == 'Ra':
          #     znum_int[i] = 88
          # elif str(spe[i][0:2]) == 'Ac':
          #     znum_int[i] = 89
          # elif str(spe[i][0:2]) == 'Th':
          #     znum_int[i] = 90
          # elif str(spe[i][0:2]) == 'Pa':
          #     znum_int[i] = 91
          # elif str(spe[i][0:2]) == 'U ':
          #     znum_int[i] = 92
          # elif str(spe[i][0:2]) == 'Np':
          #     znum_int[i] = 93
          # elif str(spe[i][0:2]) == 'Pu':
          #     znum_int[i] = 94
          # elif str(spe[i][0:2]) == 'Am':
          #     znum_int[i] = 95
          # elif str(spe[i][0:2]) == 'Cm':
          #     znum_int[i] = 96
          # elif str(spe[i][0:2]) == 'Bk':
          #     znum_int[i] = 97
          # elif str(spe[i][0:2]) == 'Cf':
          #     znum_int[i] = 98
  
      if spe[0] == 'N   1':
          znum_int[0] = 0
  
      # here the index to connect name and atomic numbers.
      global index_atomic_number
      index_atomic_number = {}
      for a,b in zip(spe,znum_int):
          index_atomic_number[a]=b