def get_species_list() -> list: """ Generates the standardized species list. Returns: list: The standardized species list initialized with xyz. """ c2h2_xyz = { 'symbols': ('C', 'C', 'H', 'H'), 'isotopes': (12, 12, 1, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.203142), (0.0, -0.0, 2.265747), (-0.0, -0.0, -1.062605)) } ch4_xyz = { 'symbols': ('C', 'H', 'H', 'H', 'H'), 'isotopes': (12, 1, 1, 1, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.08744517), (1.02525314, 0.0, -0.36248173), (-0.51262658, 0.88789525, -0.36248173), (-0.51262658, -0.88789525, -0.36248173)) } co2_xyz = { 'symbols': ('C', 'O', 'O'), 'isotopes': (12, 16, 16), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.1594846), (0.0, 0.0, -1.1594846)) } co_xyz = { 'symbols': ('O', 'C'), 'isotopes': (16, 12), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.12960815)) } f2_xyz = { 'symbols': ('F', 'F'), 'isotopes': (19, 19), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.3952041)) } ch2o_xyz = { 'symbols': ('O', 'C', 'H', 'H'), 'isotopes': (16, 12, 1, 1), 'coords': ((0.0, 0.0, 0.674622), (0.0, 0.0, -0.529707), (0.0, 0.935488, -1.109367), (0.0, -0.935488, -1.109367)) } h2o_xyz = { 'symbols': ('O', 'H', 'H'), 'isotopes': (16, 1, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.95691441), (0.92636305, 0.0, -0.23986808)) } h2_xyz = { 'symbols': ('H', 'H'), 'isotopes': (1, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.74187646)) } hcn_xyz = { 'symbols': ('C', 'N', 'H'), 'isotopes': (12, 14, 1), 'coords': ((0.0, 0.0, -0.500365), (0.0, 0.0, 0.65264), (0.0, 0.0, -1.566291)) } hf_xyz = { 'symbols': ('F', 'H'), 'isotopes': (19, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.91538107)) } n2o_xyz = { 'symbols': ('N', 'N', 'O'), 'isotopes': (14, 14, 16), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.12056262), (0.0, 0.0, 2.30761092)) } n2_xyz = { 'symbols': ('N', 'N'), 'isotopes': (14, 14), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.09710935)) } nh3_xyz = { 'symbols': ('N', 'H', 'H', 'H'), 'isotopes': (14, 1, 1, 1), 'coords': ((0.0, 0.0, 0.11289), (0.0, 0.938024, -0.263409), (0.812353, -0.469012, -0.263409), (-0.812353, -0.469012, -0.263409)) } oh_xyz = { 'symbols': ('O', 'H'), 'isotopes': (16, 1), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 0.967)) } cl2_xyz = { 'symbols': ('Cl', 'Cl'), 'isotopes': (35, 35), 'coords': ((0.0, 0.0, 0.0), (0.0, 0.0, 1.1)) } c2h2 = ARCSpecies(label='C2H2', smiles='C#C', multiplicity=1, charge=0) c2h2.initial_xyz = c2h2_xyz ch4 = ARCSpecies(label='CH4', smiles='C', multiplicity=1, charge=0) ch4.initial_xyz = ch4_xyz co2 = ARCSpecies(label='CO2', smiles='O=C=O', multiplicity=1, charge=0) co2.initial_xyz = co2_xyz co = ARCSpecies(label='CO', smiles='[C-]#[O+]', multiplicity=1, charge=0) co.initial_xyz = co_xyz f2 = ARCSpecies(label='F2', smiles='[F][F]', multiplicity=1, charge=0) f2.initial_xyz = f2_xyz ch2o = ARCSpecies(label='CH2O', smiles='C=O', multiplicity=1, charge=0) ch2o.initial_xyz = ch2o_xyz h2o = ARCSpecies(label='H2O', smiles='O', multiplicity=1, charge=0) h2o.initial_xyz = h2o_xyz h2 = ARCSpecies(label='H2', smiles='[H][H]', multiplicity=1, charge=0) h2.initial_xyz = h2_xyz hcn = ARCSpecies(label='HCN', smiles='C#N', multiplicity=1, charge=0) hcn.initial_xyz = hcn_xyz hf = ARCSpecies(label='HF', smiles='F', multiplicity=1, charge=0) hf.initial_xyz = hf_xyz n2o = ARCSpecies(label='N2O', smiles='[N-]=[N+]=O', multiplicity=1, charge=0) n2o.initial_xyz = n2o_xyz n2 = ARCSpecies(label='N2', smiles='N#N', multiplicity=1, charge=0) n2.initial_xyz = n2_xyz nh3 = ARCSpecies(label='NH3', smiles='N', multiplicity=1, charge=0) nh3.initial_xyz = nh3_xyz oh = ARCSpecies(label='OH', smiles='[OH]', multiplicity=2, charge=0) oh.initial_xyz = oh_xyz cl2 = ARCSpecies(label='Cl2', smiles='[Cl][Cl]', multiplicity=1, charge=0) cl2.initial_xyz = cl2_xyz species_list = [ c2h2, ch4, co2, co, f2, ch2o, h2o, h2, hcn, hf, n2o, n2, nh3, oh, cl2 ] return species_list
def get_species_list(): """ Generates the standardized species list. Returns: list: The standardized species list initialized with xyz. """ c2h2_xyz = """ C 0.00000000 0.00000000 0.00000000 C 0.00000000 0.00000000 1.20314200 H 0.00000000 -0.00000000 2.26574700 H -0.00000000 -0.00000000 -1.06260500""" ch4_xyz = """ C 0.00000000 0.00000000 0.00000000 H 0.00000000 0.00000000 1.08744517 H 1.02525314 0.00000000 -0.36248173 H -0.51262658 0.88789525 -0.36248173 H -0.51262658 -0.88789525 -0.36248173""" co2_xyz = """ C 0.00000000 0.00000000 0.00000000 O 0.00000000 0.00000000 1.15948460 O 0.00000000 0.00000000 -1.15948460""" co_xyz = """ O 0.00000000 0.00000000 0.00000000 C 0.00000000 0.00000000 1.12960815""" f2_xyz = """ F 0.00000000 0.00000000 0.00000000 F 0.00000000 0.00000000 1.39520410""" ch2o_xyz = """ O 0.00000000 0.00000000 0.67462200 C 0.00000000 0.00000000 -0.52970700 H 0.00000000 0.93548800 -1.10936700 H 0.00000000 -0.93548800 -1.10936700""" h2o_xyz = """ O 0.00000000 0.00000000 0.00000000 H 0.00000000 0.00000000 0.95691441 H 0.92636305 0.00000000 -0.23986808""" h2_xyz = """ H 0.00000000 0.00000000 0.00000000 H 0.00000000 0.00000000 0.74187646""" hcn_xyz = """ C 0.00000000 0.00000000 -0.50036500 N 0.00000000 0.00000000 0.65264000 H 0.00000000 0.00000000 -1.56629100""" hf_xyz = """ F 0.00000000 0.00000000 0.00000000 H 0.00000000 0.00000000 0.91538107""" n2o_xyz = """ N 0.00000000 0.00000000 0.00000000 N 0.00000000 0.00000000 1.12056262 O 0.00000000 0.00000000 2.30761092""" n2_xyz = """ N 0.00000000 0.00000000 0.00000000 N 0.00000000 0.00000000 1.09710935""" nh3_xyz = """ N 0.00000000 0.00000000 0.11289000 H 0.00000000 0.93802400 -0.26340900 H 0.81235300 -0.46901200 -0.26340900 H -0.81235300 -0.46901200 -0.26340900""" oh_xyz = """ O 0.00000000 0.00000000 0.00000000 H 0.00000000 0.00000000 0.96700000""" cl2_xyz = """ Cl 0.00000000 0.00000000 0.00000000 Cl 0.00000000 0.00000000 1.10000000""" c2h2 = ARCSpecies(label='C2H2', smiles=str('C#C'), multiplicity=1, charge=0) c2h2.initial_xyz = c2h2_xyz ch4 = ARCSpecies(label='CH4', smiles=str('C'), multiplicity=1, charge=0) ch4.initial_xyz = ch4_xyz co2 = ARCSpecies(label='CO2', smiles=str('O=C=O'), multiplicity=1, charge=0) co2.initial_xyz = co2_xyz co = ARCSpecies(label='CO', smiles=str('[C-]#[O+]'), multiplicity=1, charge=0) co.initial_xyz = co_xyz f2 = ARCSpecies(label='F2', smiles=str('[F][F]'), multiplicity=1, charge=0) f2.initial_xyz = f2_xyz ch2o = ARCSpecies(label='CH2O', smiles=str('C=O'), multiplicity=1, charge=0) ch2o.initial_xyz = ch2o_xyz h2o = ARCSpecies(label='H2O', smiles=str('O'), multiplicity=1, charge=0) h2o.initial_xyz = h2o_xyz h2 = ARCSpecies(label='H2', smiles=str('[H][H]'), multiplicity=1, charge=0) h2.initial_xyz = h2_xyz hcn = ARCSpecies(label='HCN', smiles=str('C#N'), multiplicity=1, charge=0) hcn.initial_xyz = hcn_xyz hf = ARCSpecies(label='HF', smiles=str('F'), multiplicity=1, charge=0) hf.initial_xyz = hf_xyz n2o = ARCSpecies(label='N2O', smiles=str('[N-]=[N+]=O'), multiplicity=1, charge=0) n2o.initial_xyz = n2o_xyz n2 = ARCSpecies(label='N2', smiles=str('N#N'), multiplicity=1, charge=0) n2.initial_xyz = n2_xyz nh3 = ARCSpecies(label='NH3', smiles=str('N'), multiplicity=1, charge=0) nh3.initial_xyz = nh3_xyz oh = ARCSpecies(label='OH', smiles=str('[OH]'), multiplicity=2, charge=0) oh.initial_xyz = oh_xyz cl2 = ARCSpecies(label='Cl2', smiles=str('[Cl][Cl]'), multiplicity=1, charge=0) cl2.initial_xyz = cl2_xyz species_list = [ c2h2, ch4, co2, co, f2, ch2o, h2o, h2, hcn, hf, n2o, n2, nh3, oh, cl2 ] return species_list