text: #!/usr/bin/env python3
  
  ###############################################################################
  #                                                                             #
  # RMG - Reaction Mechanism Generator                                          #
  #                                                                             #
  # Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),           #
  # Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
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  ###############################################################################
  
  """
  This module defined the chemical elements available in RMG. Information for
  each element is stored as attributes of an object of the :class:`Element`
  class.
  
  Element objects for each chemical element (1-112) have also been declared as
  module-level variables, using each element's symbol as its variable name. The
  :meth:`get_element` method can also be used to retrieve the :class:`Element`
  object associated with an atomic number or symbol. Generally applications will
  want to use these objects, both to conserve memory and to make for easy
  comparisons.
  """
  
  import cython
  from rdkit.Chem import GetPeriodicTable
  
  from rmgpy.exceptions import ElementError
  from rmgpy.quantity import Quantity
  
  ################################################################################
  
  _rdkit_periodic_table = GetPeriodicTable()
  
  
  class Element(object):
      """
      A chemical element. The attributes are:
  
      ============== =============== ================================================
      Attribute      Type            Description
      ============== =============== ================================================
      `number`       ``int``         The atomic number of the element
      `symbol`       ``str``         The symbol used for the element
      `name`         ``str``         The IUPAC name of the element
      `mass`         ``float``       The mass of the element in kg/mol
      `cov_radius`   ``float``       Covalent bond radius in Angstrom
      `isotope`      ``int``         The isotope integer of the element
      `chemkin_name` ``str``         The chemkin compatible representation of the element
      ============== =============== ================================================
  
      This class is specifically for properties that all atoms of the same element
      share. Ideally there is only one instance of this class for each element.
      """
  
      def __init__(self, number, symbol, name, mass, isotope=-1, chemkin_name=None):
          self.number = number
          self.symbol = symbol
          self.name = name
          self.mass = mass
          self.isotope = isotope
          self.chemkin_name = chemkin_name or self.name
          if symbol == 'X':
              self.cov_radius = 0
          else:
              try:
                  self.cov_radius = _rdkit_periodic_table.GetRcovalent(symbol)
              except RuntimeError:
                  import logging
                  logging.error("RDkit doesn't know element {0} so covalent radius unknown".format(symbol))
                  self.cov_radius = 0
  
      def __str__(self):
          """
          Return a human-readable string representation of the object.
          """
          return self.symbol
  
      def __repr__(self):
          """
          Return a representation that can be used to reconstruct the object.
          """
          return "Element(%s, '%s', '%s', %s, %s)" % (self.number, self.symbol, self.name, self.mass, self.isotope)
  
      def __reduce__(self):
          """
          A helper function used when pickling an object.
          """
          return (Element, (self.number, self.symbol, self.name, self.mass, self.isotope))
  
  
  class PeriodicSystem(object):
      """
      Collects hard-coded information of elements in periodic table.
  
      Currently it has static attributes:
      `valences`: the number of bonds an element is able to form around it.
      `valence_electrons`: the number of electrons in  the outermost shell of the element that can
      participate in bond formation. for instance, `S` has 6 outermost electrons (valence_electrons)
      but 4 of them form lone pairs, the remaining 2 electrons can form bonds so the normal valence
      for `S` is 2.
      `lone_pairs`: the number of lone pairs an element has
      'electronegativity': The atom's electronegativity (how well can an atom attract electrons), taken from
      https://sciencenotes.org/list-of-electronegativity-values-of-the-elements/
      isotopes of the same element may have slight different electronegativities, which is not reflected below
      """
      valences = {'H': 1, 'He': 0, 'C': 4, 'N': 3, 'O': 2, 'F': 1, 'Ne': 0,
                  'Si': 4, 'S': 2, 'Cl': 1, 'Br': 1, 'Ar': 0, 'I': 1, 'X': 4}
      valence_electrons = {'H': 1, 'He': 2, 'C': 4, 'N': 5, 'O': 6, 'F': 7, 'Ne': 8,
                           'Si': 4, 'S': 6, 'Cl': 7, 'Br': 7, 'Ar': 8, 'I': 7, 'X': 4}
      lone_pairs = {'H': 0, 'He': 1, 'C': 0, 'N': 1, 'O': 2, 'F': 3, 'Ne': 4,
                    'Si': 0, 'S': 2, 'Cl': 3, 'Br': 3, 'Ar': 4, 'I': 3, 'X': 0}
      electronegativity = {'H': 2.20, 'D': 2.20, 'T': 2.20, 'C': 2.55, 'C13': 2.55, 'N': 3.04, 'O': 3.44, 'O18': 3.44,
                           'F': 3.98, 'Si': 1.90, 'S': 2.58, 'Cl': 3.16, 'Br': 2.96, 'I': 2.66, 'X': 0.0}
  
  
  ################################################################################
  
  
  def get_element(value, isotope=-1):
      """
      Return the :class:`Element` object corresponding to the given parameter
      `value`. If an integer is provided, the value is treated as the atomic
      number. If a string is provided, the value is treated as the symbol. An
      :class:`ElementError` is raised if no matching element is found.
      """
      cython.declare(element=Element, number=cython.int, symbol=str)
      if isinstance(value, int):
          # The parameter is an integer; assume this is the atomic number
          number = value
          for element in element_list:
              if element.number == number and element.isotope == isotope:
                  return element
          # If we reach this point that means we did not find an appropriate element,
          # so we raise an exception
          raise ElementError("No element found with atomic number %i, and isotope %i" % (number, isotope))
      elif isinstance(value, str):
          # The parameter is a string; assume this is the element symbol
          symbol = value
          for element in element_list:
              if element.symbol == symbol and element.isotope == isotope:
                  return element
          # If we reach this point that means we did not find an appropriate element,
          # so we raise an exception
          raise ElementError("No element found with symbol %s, and isotope %i." % (symbol, isotope))
      else:
          raise ElementError('No element found based on parameter %s "%r", isotope: %i.' % (type(value), value, isotope))
  
  
  ################################################################################
  
  # Declare an instance of each element (1 to 112)
  # The variable names correspond to each element's symbol
  # The elements are sorted by increasing atomic number and grouped by period
  # Recommended IUPAC nomenclature is used throughout (including 'aluminium' and
  # 'caesium')
  
  
  # Surface site
  X = Element(0,    'X', 'surface_site'   , 0.0)
  
  # Period 1
  # Hydrogen
  H  = Element(1,   'H' , 'hydrogen'      , 0.00100794)
  D  = Element(1,   'H' , 'deuterium'     , 0.002014101, 2, 'D')
  T  = Element(1,   'H' , 'tritium'       , 0.003016049, 3, 'T')
  He = Element(2,   'He', 'helium'        , 0.004002602)
  
  # Period 2
  Li = Element(3,   'Li', 'lithium'       , 0.006941)
  Be = Element(4,   'Be', 'beryllium'     , 0.009012182)
  B  = Element(5,   'B',  'boron'         , 0.010811)
  C  = Element(6,   'C' , 'carbon'        , 0.0120107)
  C13= Element(6,   'C' , 'carbon-13'     , 0.0130033, 13, 'CI')
  N  = Element(7,   'N' , 'nitrogen'      , 0.01400674)
  O  = Element(8,   'O' , 'oxygen'        , 0.0159994)
  O18= Element(8,   'O' , 'oxygen-18'     , 0.0179999, 18, 'OI')
  F  = Element(9,   'F' , 'fluorine'      , 0.018998403)
  Ne = Element(10,  'Ne', 'neon'          , 0.0201797)
  
  # Period 3
  Na = Element(11,  'Na', 'sodium'        , 0.022989770)
  Mg = Element(12,  'Mg', 'magnesium'     , 0.0243050)
  Al = Element(13,  'Al', 'aluminium'     , 0.026981538)
  Si = Element(14,  'Si', 'silicon'       , 0.0280855)
  P  = Element(15,  'P' , 'phosphorus'    , 0.030973761)
  S  = Element(16,  'S' , 'sulfur'        , 0.032065)
  Cl = Element(17,  'Cl', 'chlorine'      , 0.035453)
  Ar = Element(18,  'Ar', 'argon'         , 0.039348)
  
  # Period 4
  K  = Element(19,  'K' , 'potassium'     , 0.0390983)
  Ca = Element(20,  'Ca', 'calcium'       , 0.040078)
  Sc = Element(21,  'Sc', 'scandium'      , 0.044955910)
  Ti = Element(22,  'Ti', 'titanium'      , 0.047867)
  V  = Element(23,  'V' , 'vanadium'      , 0.0509415)
  Cr = Element(24,  'Cr', 'chromium'      , 0.0519961)
  Mn = Element(25,  'Mn', 'manganese'     , 0.054938049)
  Fe = Element(26,  'Fe', 'iron'          , 0.055845)
  Co = Element(27,  'Co', 'cobalt'        , 0.058933200)
  Ni = Element(28,  'Ni', 'nickel'        , 0.0586934)
  Cu = Element(29,  'Cu', 'copper'        , 0.063546)
  Zn = Element(30,  'Zn', 'zinc'          , 0.065409)
  Ga = Element(31,  'Ga', 'gallium'       , 0.069723)
  Ge = Element(32,  'Ge', 'germanium'     , 0.07264)
  As = Element(33,  'As', 'arsenic'       , 0.07492160)
  Se = Element(34,  'Se', 'selenium'      , 0.07896)
  Br = Element(35,  'Br', 'bromine'       , 0.079904)
  Kr = Element(36,  'Kr', 'krypton'       , 0.083798)
  
  # Period 5
  Rb = Element(37,  'Rb', 'rubidium'      , 0.0854678)
  Sr = Element(38,  'Sr', 'strontium'     , 0.08762)
  Y  = Element(39,  'Y' , 'yttrium'       , 0.08890585)
  Zr = Element(40,  'Zr', 'zirconium'     , 0.091224)
  Nb = Element(41,  'Nb', 'niobium'       , 0.09290638)
  Mo = Element(42,  'Mo', 'molybdenum'    , 0.09594)
  Tc = Element(43,  'Tc', 'technetium'    , 0.098)
  Ru = Element(44,  'Ru', 'ruthenium'     , 0.10107)
  Rh = Element(45,  'Rh', 'rhodium'       , 0.10290550)
  Pd = Element(46,  'Pd', 'palladium'     , 0.10642)
  Ag = Element(47,  'Ag', 'silver'        , 0.1078682)
  Cd = Element(48,  'Cd', 'cadmium'       , 0.112411)
  In = Element(49,  'In', 'indium'        , 0.114818)
  Sn = Element(50,  'Sn', 'tin'           , 0.118710)
  Sb = Element(51,  'Sb', 'antimony'      , 0.121760)
  Te = Element(52,  'Te', 'tellurium'     , 0.12760)
  I  = Element(53,  'I' , 'iodine'        , 0.12690447)
  Xe = Element(54,  'Xe', 'xenon'         , 0.131293)
  
  # Period 6
  Cs = Element(55,  'Cs', 'caesium'       , 0.13290545)
  Ba = Element(56,  'Ba', 'barium'        , 0.137327)
  La = Element(57,  'La', 'lanthanum'     , 0.1389055)
  Ce = Element(58,  'Ce', 'cerium'        , 0.140116)
  Pr = Element(59,  'Pr', 'praesodymium'  , 0.14090765)
  Nd = Element(60,  'Nd', 'neodymium'     , 0.14424)
  Pm = Element(61,  'Pm', 'promethium'    , 0.145)
  Sm = Element(62,  'Sm', 'samarium'      , 0.15036)
  Eu = Element(63,  'Eu', 'europium'      , 0.151964)
  Gd = Element(64,  'Gd', 'gadolinium'    , 0.15725)
  Tb = Element(65,  'Tb', 'terbium'       , 0.15892534)
  Dy = Element(66,  'Dy', 'dysprosium'    , 0.162500)
  Ho = Element(67,  'Ho', 'holmium'       , 0.16493032)
  Er = Element(68,  'Er', 'erbium'        , 0.167259)
  Tm = Element(69,  'Tm', 'thulium'       , 0.16893421)
  Yb = Element(70,  'Yb', 'ytterbium'     , 0.17304)
  Lu = Element(71,  'Lu', 'lutetium'      , 0.174967)
  Hf = Element(72,  'Hf', 'hafnium'       , 0.17849)
  Ta = Element(73,  'Ta', 'tantalum'      , 0.1809479)
  W  = Element(74,  'W' , 'tungsten'      , 0.18384)
  Re = Element(75,  'Re', 'rhenium'       , 0.186207)
  Os = Element(76,  'Os', 'osmium'        , 0.19023)
  Ir = Element(77,  'Ir', 'iridium'       , 0.192217)
  Pt = Element(78,  'Pt', 'platinum'      , 0.195078)
  Au = Element(79,  'Au', 'gold'          , 0.19696655)
  Hg = Element(80,  'Hg', 'mercury'       , 0.20059)
  Tl = Element(81,  'Tl', 'thallium'      , 0.2043833)
  Pb = Element(82,  'Pb', 'lead'          , 0.2072)
  Bi = Element(83,  'Bi', 'bismuth'       , 0.20898038)
  Po = Element(84,  'Po', 'polonium'      , 0.209)
  At = Element(85,  'At', 'astatine'      , 0.210)
  Rn = Element(86,  'Rn', 'radon'         , 0.222)
  
  # Period 7
  Fr = Element(87,  'Fr', 'francium'      , 0.223)
  Ra = Element(88,  'Ra', 'radium'        , 0.226)
  Ac = Element(89,  'Ac', 'actinum'       , 0.227)
  Th = Element(90,  'Th', 'thorium'       , 0.2320381)
  Pa = Element(91,  'Pa', 'protactinum'   , 0.23103588)
  U  = Element(92,  'U' , 'uranium'       , 0.23802891)
  Np = Element(93,  'Np', 'neptunium'     , 0.237)
  Pu = Element(94,  'Pu', 'plutonium'     , 0.244)
  Am = Element(95,  'Am', 'americium'     , 0.243)
  Cm = Element(96,  'Cm', 'curium'        , 0.247)
  Bk = Element(97,  'Bk', 'berkelium'     , 0.247)
  Cf = Element(98,  'Cf', 'californium'   , 0.251)
  Es = Element(99,  'Es', 'einsteinium'   , 0.252)
  Fm = Element(100, 'Fm', 'fermium'       , 0.257)
  Md = Element(101, 'Md', 'mendelevium'   , 0.258)
  No = Element(102, 'No', 'nobelium'      , 0.259)
  Lr = Element(103, 'Lr', 'lawrencium'    , 0.262)
  Rf = Element(104, 'Rf', 'rutherfordium' , 0.261)
  Db = Element(105, 'Db', 'dubnium'       , 0.262)
  Sg = Element(106, 'Sg', 'seaborgium'    , 0.266)
  Bh = Element(107, 'Bh', 'bohrium'       , 0.264)
  Hs = Element(108, 'Hs', 'hassium'       , 0.277)
  Mt = Element(109, 'Mt', 'meitnerium'    , 0.268)
  Ds = Element(110, 'Ds', 'darmstadtium'  , 0.281)
  Rg = Element(111, 'Rg', 'roentgenium'   , 0.272)
  Cn = Element(112, 'Cn', 'copernicum'    , 0.285)
  
  # A list of the elements, sorted by increasing atomic number
  element_list = [
      X,
      H, D, T, He,
      Li, Be, B, C, C13, N, O, O18, F, Ne,
      Na, Mg, Al, Si, P, S, Cl, Ar,
      K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr,
      Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe,
      Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi,
      Po, At, Rn,
      Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg, Cn
  ]
  
  # Bond Dissociation Energies
  # References:
  # Huheey, pps. A-21 to A-34; T.L. Cottrell, "The Strengths of Chemical Bonds," 2nd ed., Butterworths, London, 1958
  # B. deB. Darwent, "National Standard Reference Data Series," National Bureau of Standards, No. 31, Washington, DC, 1970
  # S.W. Benson, J. Chem. Educ., 42, 502 (1965)
  # (C,C,1.5) was taken from an unsourced table that had similar values to those used below, should be replaced
  # if a sourced value becomes available
  # (C,C,2.5) is C#C - (CbenzeneC - C-C)
  bde_elements = ['C', 'N', 'H', 'O', 'S', 'Cl', 'Si']  # elements supported by BDE
  bde_dict = {('H', 'H', 1.0): (432.0, 'kJ/mol'), ('H', 'C', 1): (411.0, 'kJ/mol'),
              ('H', 'N', 1): (386.0, 'kJ/mol'), ('H', 'O', 1.0): (459.0, 'kJ/mol'),
              ('H', 'S', 1): (363.0, 'kJ/mol'), ('H', 'Cl', 1): (428.0, 'kJ/mol'),
              ('C', 'C', 1): (346.0, 'kJ/mol'), ('C', 'C', 2): (602.0, 'kJ/mol'),
              ('C', 'C', 3): (835.0, 'kJ/mol'), ('C', 'Si', 1): (318.0, 'kJ/mol'),
              ('C', 'N', 1): (305.0, 'kJ/mol'), ('C', 'N', 2): (615.0, 'kJ/mol'),
              ('C', 'N', 3): (887.0, 'kJ/mol'), ('C', 'O', 1): (358.0, 'kJ/mol'),
              ('C', 'O', 2): (799.0, 'kJ/mol'), ('C', 'O', 3): (1072.0, 'kJ/mol'),
              ('C', 'S', 1): (272.0, 'kJ/mol'), ('C', 'S', 2): (573.0, 'kJ/mol'),
              ('C', 'Cl', 1): (327.0, 'kJ/mol'), ('Si', 'Si', 1): (222.0, 'kJ/mol'),
              ('Si', 'N', 1): (355.0, 'kJ/mol'), ('Si', 'O', 1): (452.0, 'kJ/mol'),
              ('Si', 'S', 1): (293.0, 'kJ/mol'), ('Si', 'Cl', 1): (381.0, 'kJ/mol'),
              ('N', 'N', 1): (167.0, 'kJ/mol'), ('N', 'N', 2): (418.0, 'kJ/mol'),
              ('N', 'N', 3): (942.0, 'kJ/mol'), ('N', 'O', 1): (201.0, 'kJ/mol'),
              ('N', 'O', 2): (607.0, 'kJ/mol'), ('N', 'Cl', 1): (313.0, 'kJ/mol'),
              ('O', 'O', 1): (142.0, 'kJ/mol'), ('O', 'O', 2): (494.0, 'kJ/mol'),
              ('S', 'O', 2): (522.0, 'kJ/mol'), ('S', 'S', 1): (226.0, 'kJ/mol'),
              ('S', 'S', 2): (425.0, 'kJ/mol'), ('S', 'Cl', 1): (255.0, 'kJ/mol'),
              ('Cl', 'Cl', 1): (240.0, 'kJ/mol'), ('C', 'C', 1.5): (518.0, 'kJ/mol'),
              ('O', 'S', 1): (265.0, 'kJ/mol'), ('C', 'C', 2.5): (663.0, 'kJ/mol')}
  
  bdes = {}
  for key, value in bde_dict.items():
      q = Quantity(value).value_si
      bdes[(key[0], key[1], key[2])] = q
      bdes[(key[1], key[0], key[2])] = q
  