# Trough mechanism from 'S. J. Harris and D. G. Goodwin, 'Growth on
# the reconstructed diamond (100) surface, 'J. Phys. Chem. vo. 97,
# 23-28 (1993). reactions a - t are taken directly from Table II,
# with thermochemistry from Table IV. Reaction u is added here.


units(length = 'cm', quantity = 'mol', act_energy = 'kcal/mol')

#------------- the gas -------------------------------------

ideal_gas(name = 'gas',
          elements = 'H C',
          species = 'gri30: H H2 CH3 CH4',
          initial_state = state(temperature = 1200.0,
                                pressure = 20.0*OneAtm/760.0,
                    mole_fractions = 'H:0.002, H2:0.988, CH3:0.0002, CH4:0.01'))


#------------- bulk diamond -------------------------------------

stoichiometric_solid(name = 'diamond',
                     elements = 'H C',
                     density = (3.52, 'g/cm3'),
                     species = 'C(d)')

species(name = 'C(d)',
        atoms = 'C:1')   #no thermo needed (rxn is ireversible) 


#------------- the diamond surface -------------------------------------

ideal_interface(name = 'diamond_100',
	        elements = ' H C ',
	        species = 'c6HH c6H* c6*H c6** c6HM c6HM* c6*M c6B',
                reactions = 'all',
                phases = 'gas diamond',
                site_density = (3.0E-9, 'mol/cm2'),
                initial_state = state(temperature= 1200.0,
                                      coverages = 'c6H*:0.1, c6HH:0.9'))


species(name = 'c6H*',
        atoms = 'H:1',
        thermo = const_cp(h0 = (51.7, 'kcal/mol'),
                          s0 = (19.5, 'cal/mol/K') ) )

species(name = 'c6*H',
        atoms = 'H:1',
        thermo = const_cp(h0 = (46.1, 'kcal/mol'),
                          s0 = (19.9, 'cal/mol/K') ) )

species(name = 'c6HH',
        atoms = 'H:2',
        thermo = const_cp(h0 = (11.4, 'kcal/mol'),
                          s0 = (21.0, 'cal/mol/K') ) )

species(name = 'c6HM',
        atoms = 'C:1 H:4',
        thermo = const_cp(h0 = (26.9, 'kcal/mol'),
                          s0 = (40.3, 'cal/mol/K') ) )

species(name = 'c6HM*',
        atoms = 'C:1 H:3',
        thermo = const_cp(h0 = (65.8, 'kcal/mol'),
                          s0 = (40.1, 'cal/mol/K') ) )

species(name = 'c6*M',
        atoms = 'C:1 H:3',
        thermo = const_cp(h0 = (53.3, 'kcal/mol'),
                          s0 = (38.9, 'cal/mol/K') ) )

species(name = 'c6**',
        atoms = 'C:0',
        thermo = const_cp(h0 = (90.0, 'kcal/mol'),
                          s0 = (18.4, 'cal/mol/K') ) )

species(name = 'c6B',
        atoms = 'H:2 C:1',
        thermo = const_cp(h0 = (40.9, 'kcal/mol'),
                          s0 = (26.9, 'cal/mol/K') ) )



surface_reaction( 'c6HH + H   <=> c6H* + H2',       [1.3E14, 0.0, 7.3]) #a
surface_reaction( 'c6H* + H   <=> c6HH',            [1.0E13, 0.0, 0.0]) #b
surface_reaction( 'c6H* + CH3 <=> c6HM',            [5.0E12, 0.0, 0.0]) #c
surface_reaction( 'c6HM + H   <=> c6*M + H2',       [1.3E14, 0.0, 7.3]) #d
surface_reaction( 'c6*M + H   <=> c6HM',            [1.0E13, 0.0, 0.0]) #e
surface_reaction( 'c6HM + H   <=> c6HM* + H2',      [2.8E7,  0.0, 7.7]) #f
surface_reaction( 'c6HM* + H  <=> c6HM',            [1.0E13, 0.0, 0.0]) #g
surface_reaction( 'c6HM*      <=> c6*M',            [1.0E8,  0.0, 0.0]) #h
surface_reaction( 'c6HM* + H  <=> c6H* + CH3',      [3.0E13, 0.0, 0.0]) #i
surface_reaction( 'c6HM* + H  <=> c6B + H2',        [1.3E14, 0.0, 7.3]) #k
surface_reaction( 'c6*M + H   <=> c6B + H2',        [2.8E7,  2.0, 7.7]) #l
surface_reaction( 'c6HH + H   <=> c6*H + H2',       [1.3E14, 0.0, 7.3]) #m
surface_reaction( 'c6*H + H   <=> c6HH',            [1.0E13, 0.0, 0.0]) #m
surface_reaction( 'c6H* + H   <=> c6** + H2',       [1.3E14, 0.0, 7.3]) #o
surface_reaction( 'c6** + H   <=> c6H*',            [1.0E13, 0.0, 0.0]) #p
surface_reaction( 'c6*H + H   <=> c6** + H2',       [4.5E6,  2.0, 5.0]) #q
surface_reaction( 'c6** + H   <=> c6*H',            [1.0E13, 0.0, 0.0]) #r
surface_reaction( 'c6** + CH3 <=> c6*M',            [5.0E12, 0.0, 0.0]) #s
surface_reaction( 'c6H*       <=> c6*H',            [1.0E8,  0.0, 0.0]) #t

# reaction to add new carbon atom to bulk and regenerate a new site
#
surface_reaction( 'c6B       <=> c6HH + C(d)',      [1.0E9,  0.0, 0.0]) #u