def test_linear_ts():
"""
compute a first approximation to the TS.
"""
# Read the Molecule from file
cnc = Molecule('test/test_files/C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "SZ"
settings.specific.dftb.dftb.scc
constraint1 = Distance(0, 4)
constraint2 = Distance(2, 3)
# scan input
pes = PES(cnc,
constraints=[constraint1, constraint2],
offset=[2.3, 2.3],
get_current_values=False,
nsteps=2,
stepsize=[0.1, 0.1])
# returns a set of results object containing the output of
# each point in the scan
lt = pes.scan([dftb, adf], settings)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
# Run the TS optimization, using the default TS template
ts = run(apprTS)
expected_energy = -3.219708290363864
assert abs(ts.energy - expected_energy) < 0.02
def bond_distance(r1, r2):
return sqrt(sum((x - y)**2 for x, y in zip(r1, r2)))
# ========== =============
plams.init()
# Read the Molecule from file
cnc = Molecule('C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "TZ2P"
settings.specific.dftb.dftb.scc
constraint1 = "dist 1 5"
constraint2 = "dist 3 4"
# scan input
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 6,
'start': [2.3, 2.3],
'stepsize': [0.1, 0.1]
}
}