def get_lmethod():
"""Get the low-level electronic structure theory method to use
Returns:
(autode.wrappers.base.ElectronicStructureMethod):
"""
all_methods = [XTB(), MOPAC(), ORCA(), G16(), G09(), NWChem()]
if Config.lcode is not None:
return get_defined_method(name=Config.lcode.lower(),
possibilities=all_methods)
else:
return get_first_available_method(all_methods)
def get_hmethod():
"""Get the high-level electronic structure theory method to use
Returns:
(autode.wrappers.base.ElectronicStructureMethod): Method
"""
orca = ORCA()
g09 = G09()
nwchem = NWChem()
g16 = G16()
if Config.hcode is not None:
return get_defined_method(name=Config.hcode.lower(),
possibilities=[orca, g16, g09, nwchem])
else:
return get_first_available_method([orca, g16, g09, nwchem])
def test_correct_imag_mode():
os.chdir(os.path.join(here, 'data'))
bond_rearrangement = BondRearrangement(breaking_bonds=[(4, 1), (4, 18)],
forming_bonds=[(1, 18)])
g09 = G09()
g09.available = True
calc = Calculation(name='tmp',
molecule=ReactantComplex(
Reactant(smiles='CC(C)(C)C1C=CC=C1')),
method=g09,
keywords=Config.G09.keywords.opt_ts)
calc.output.filename = 'correct_ts_mode_g09.log'
calc.output.set_lines()
f_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=1.0)
f_species = Species(name='f_displaced',
atoms=f_displaced_atoms,
charge=0,
mult=1) # Charge & mult are placeholders
b_displaced_atoms = get_displaced_atoms_along_mode(calc,
mode_number=6,
disp_magnitude=-1.0)
b_species = Species(name='b_displaced',
atoms=b_displaced_atoms,
charge=0,
mult=1)
# With the correct mode no other bonds are made
assert not imag_mode_generates_other_bonds(
ts=calc.molecule,
f_species=f_species,
b_species=b_species,
bond_rearrangement=bond_rearrangement)
calc.output.filename = 'incorrect_ts_mode_g09.log'
calc.output.set_lines()
assert not imag_mode_has_correct_displacement(calc, bond_rearrangement)
os.chdir(here)
from autode.wrappers.G09 import G09
from autode.calculation import Calculation
from autode.species.molecule import Molecule
from autode.wrappers.keywords import OptKeywords, SinglePointKeywords
from autode.exceptions import AtomsNotFound
from autode.exceptions import NoInputError
from autode.exceptions import NoNormalModesFound
from autode.point_charges import PointCharge
import pytest
import os
import numpy as np
here = os.path.dirname(os.path.abspath(__file__))
test_mol = Molecule(name='methane', smiles='C')
method = G09()
method.available = True
opt_keywords = OptKeywords(['PBE1PBE/Def2SVP', 'Opt'])
optts_keywords = OptKeywords([
'PBE1PBE/Def2SVP', 'Freq', 'Opt=(TS, CalcFC, NoEigenTest, '
'MaxCycles=100, MaxStep=10, NoTrustUpdate)'
])
sp_keywords = SinglePointKeywords(['PBE1PBE/Def2SVP'])
def test_gauss_opt_calc():
os.chdir(os.path.join(here, 'data'))
methylchloride = Molecule(name='CH3Cl',