def test_sum_mep():
reactant = ReactantComplex(Molecule(smiles='C', charge=0, mult=1))
product = ProductComplex(Molecule(smiles='C', charge=0, mult=1))
product.graph.remove_edge(0, 1)
product.graph.remove_edge(0, 2)
# Fictitious PES
pes = PES2d(reactant,
product,
r1s=np.linspace(1, 2, 3),
r1_idxs=(0, 1),
r2s=np.linspace(1, 2, 3),
r2_idxs=(0, 2))
# Energies are all 0 apart from at the 'saddle point' (1, 1)
for i in range(3):
for j in range(3):
pes.species[i, j] = deepcopy(reactant)
pes.species[i, j].energy = 0
if i == j == 2:
pes.species[i, j].graph = product.graph
pes.species[1, 1].energy = 1
mep_sum = mep.get_sum_energy_mep(saddle_point_r1r2=(1.5, 1.5), pes_2d=pes)
# Energy over the saddle point is 1 both sides -> 2 Ha
assert mep_sum == 2
def test_get_closest_species():
assert type(get_closest_species(pes=pes, point=(0, 0))) is ReactantComplex
assert type(get_closest_species(pes=pes, point=(1, 1))) is ReactantComplex
pes2 = PES2d(reactant=reactant, product=product,
r1s=np.linspace(1, 5, 5), r1_idxs=(0, 1),
r2s=np.linspace(1, 5, 5), r2_idxs=(2, 3))
with pytest.raises(NoClosestSpecies):
get_closest_species(pes=pes2, point=(4, 4))
from autode.mol_graphs import make_graph
from autode.exceptions import NoClosestSpecies
from autode.pes.pes import FormingBond, BreakingBond
from autode.reactions.reaction import Reaction
from autode.species.molecule import Reactant, Product
import pytest
import numpy as np
mol = Species(name='H2', charge=0, mult=1, atoms=[Atom('H'), Atom('H', z=1.0)])
make_graph(mol)
reactant = ReactantComplex(mol, mol)
product = ProductComplex(mol, mol)
pes = PES2d(reactant=reactant,
product=reactant,
r1s=np.linspace(1, 3, 3),
r1_idxs=(0, 1),
r2s=np.linspace(1, 0, 2),
r2_idxs=(2, 3))
def test_2d_pes_class():
assert reactant.n_atoms == 4
assert pes.rs.shape == (3, 2)
assert pes.species.shape == (3, 2)
assert pes.rs[0, 0] == (1, 1)
assert pes.rs[1, 1] == (2, 0)
assert pes.rs[2, 1] == (3, 0)