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
