def test_reaction_class():
h1 = reaction.Reactant(name='h1', atoms=[Atom('H', 0.0, 0.0, 0.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.7, 0.0, 0.0)])
# h + h > mol
hh_reac = reaction.Reaction(h1, h2, hh_product, name='h2_assoc')
h1.energy = 2
h2.energy = 3
hh_product.energy = 1
# Only swap to dissociation in invoking locate_ts()
assert hh_reac.type == reaction_types.Addition
assert len(hh_reac.prods) == 1
assert len(hh_reac.reacs) == 2
assert hh_reac.ts is None
assert hh_reac.tss is None
assert hh_reac.name == 'h2_assoc'
assert hh_reac.calc_delta_e() == -4
h1 = reaction.Reactant(name='h1', atoms=[Atom('H')])
hh_reactant = reaction.Reactant(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
# h + mol > mol + h
h_sub = reaction.Reaction(h1, hh_reactant, h2_product, hh_product,
solvent_name='water')
assert h_sub.type == reaction_types.Substitution
assert h_sub.name == 'reaction'
assert h_sub.solvent.name == 'water'
assert h_sub.solvent.smiles == 'O'
def test_bad_balance():
hh_product = reaction.Product(name='hh',
atoms=[Atom('H'),
Atom('H', x=1.0)])
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, hh_product)
h_minus = reaction.Reactant(name='h1_minus', atoms=[Atom('H')], charge=-1)
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, h_minus, hh_product)
h1_water = reaction.Reactant(name='h1',
atoms=[Atom('H')],
solvent_name='water')
h2_water = reaction.Reactant(name='h2',
atoms=[Atom('H', x=1.0)],
solvent_name='water')
hh_thf = reaction.Product(name='hh',
atoms=[Atom('H'), Atom('H', x=1.0)],
solvent_name='thf')
with pytest.raises(SolventsDontMatch):
reaction.Reaction(h1_water, h2_water, hh_thf)
with pytest.raises(NotImplementedError):
hh_triplet = reaction.Product(name='hh_trip',
atoms=[Atom('H'),
Atom('H', x=0.7)],
mult=3)
reaction.Reaction(h1, h2, hh_triplet)
def test_calc_delta_e():
r1 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r1.energy = -0.5
r2 = reaction.Reactant(name='h', atoms=[Atom('H', 0.0, 0.0, 0.0)])
r2.energy = -0.5
tsguess = TSguess(atoms=None,
reactant=ReactantComplex(r1),
product=ProductComplex(r2))
tsguess.bond_rearrangement = BondRearrangement()
ts = TransitionState(tsguess)
ts.energy = -0.8
p = reaction.Product(
name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)])
p.energy = -1.0
reac = reaction.Reaction(r1, r2, p)
reac.ts = ts
assert -1E-6 < reac.calc_delta_e() < 1E-6
assert 0.2 - 1E-6 < reac.calc_delta_e_ddagger() < 0.2 + 1E-6
def test_bad_balance():
hh_product = reaction.Product(
name='hh', atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)])
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, hh_product)
h_minus = reaction.Reactant(name='h1_minus',
atoms=[Atom('H', 0.0, 0.0, 0.0)],
charge=-1)
with pytest.raises(UnbalancedReaction):
reaction.Reaction(h1, h_minus, hh_product)
h1_water = reaction.Reactant(name='h1',
atoms=[Atom('H', 0.0, 0.0, 0.0)],
solvent_name='water')
h2_water = reaction.Reactant(name='h2',
atoms=[Atom('H', 1.0, 0.0, 0.0)],
solvent_name='water')
hh_thf = reaction.Product(
name='hh',
atoms=[Atom('H', 0.0, 0.0, 0.0),
Atom('H', 1.0, 0.0, 0.0)],
solvent_name='thf')
with pytest.raises(SolventsDontMatch):
reaction.Reaction(h1_water, h2_water, hh_thf)
def test_unavail_properties():
ha = reaction.Reactant(name='ha', atoms=[Atom('H')])
hb = reaction.Product(name='hb', atoms=[Atom('H')])
rxn = reaction.Reaction(ha, hb)
delta = reaction.calc_delta_with_cont(left=[ha], right=[hb], cont='h_cont')
assert delta is None
# Should not raise an exception(?)
rxn.find_lowest_energy_ts_conformer()
rxn.calculate_thermochemical_cont(free_energy=False, enthalpy=False)
def test_reaction_identical_reac_prods():
os.chdir(os.path.join(here, 'data'))
hh_reactant = reaction.Reactant(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
hh_product = reaction.Product(name='hh', atoms=[Atom('H'),
Atom('H', x=1.0)])
h2_reaction = reaction.Reaction(hh_reactant, hh_product)
h2_reaction.locate_transition_state()
assert h2_reaction.ts is None
shutil.rmtree('transition_states')
os.chdir(here)
from autode.exceptions import UnbalancedReaction
from autode.exceptions import SolventsDontMatch
from autode.mol_graphs import make_graph
from autode.plotting import plot_reaction_profile
from autode.units import KcalMol
from autode.methods import get_hmethod
from autode.config import Config
from autode.constants import Constants
from .testutils import work_in_zipped_dir
import shutil
import pytest
here = os.path.dirname(os.path.abspath(__file__))
Config.keyword_prefixes = False
h1 = reaction.Reactant(name='h1', atoms=[Atom('H', 0.0, 0.0, 0.0)])
h2 = reaction.Reactant(name='h2', atoms=[Atom('H', 1.0, 0.0, 0.0)])
h2_product = reaction.Product(name='h2', atoms=[Atom('H', 1.0, 0.0, 0.0)])
lin_h3 = reaction.Reactant(name='h3_linear',
atoms=[
Atom('H', -1.76172, 0.79084, -0.00832),
Atom('H', -2.13052, 0.18085, 0.00494),
Atom('H', -1.39867, 1.39880, -0.00676)
])
trig_h3 = reaction.Product(name='h3_trigonal',
atoms=[
Atom('H', -1.76172, 0.79084, -0.00832),
Atom('H', -1.65980, 1.15506, 0.61469),
