def test_ts_hessian_opt():
geom = geom_loader("lib:baker_ts/01_hcn.xyz", coord_type="redund")
geom.set_calculator(PySCF(basis="321g"))
opt_kwargs = {
"hessian_init": "fischer",
"dump": True,
"rx_coords": ((2, 1, 0), ),
"thresh": "gau_tight",
}
opt = RSPRFOptimizer(geom, **opt_kwargs)
opt.run()
do_final_hessian(geom, write_imag_modes=True)
assert opt.is_converged
assert opt.cur_cycle == 11
assert geom.energy == pytest.approx(-92.2460426792319)
def test_baker_ts_dimer(name, geom, charge, mult, ref_energy):
print(f"@Got geom '{name}'")
# Load initial dimers
N_init_dict = make_N_init_dict()
calc_kwargs = {
"charge": charge,
"mult": mult,
"pal": 2,
"base_name": Path(name).stem,
}
def calc_getter():
return PySCF(basis="321g", **calc_kwargs)
# def calc_getter():
# return Gaussian16(route="HF/3-21G", **calc_kwargs)
geom.set_calculator(calc_getter())
dimer_kwargs = {
"max_step": 0.25,
# 1e-2 Angstroem in bohr
"dR_base": 0.0189,
"rot_opt": "lbfgs",
# "trans_opt": "mb",
"trans_opt": "lbfgs",
# "trans_memory": 10, # bad idea
"angle_tol": 5,
"f_thresh": 1e-3,
"max_cycles": 50,
"f_tran_mod": True,
# "rot_type": "direct",
"multiple_translations": True,
}
dimer_kwargs["N_init"] = N_init_dict[name]
geoms = (geom, )
results = dimer_method(geoms, calc_getter, **dimer_kwargs)
same_energy = geom.energy == pytest.approx(ref_energy)
print(f"@Same energy: {str(same_energy): >5}, {name}, "
f"{results.force_evals} force evaluations")
if not same_energy:
do_final_hessian(geom)
# This way pytest prints the actual values... instead of just the boolean
assert geom.energy == pytest.approx(ref_energy)
def test_ts_hessian_opt(tsopt_cls, ref_cycle):
geom = geom_loader("lib:baker_ts/01_hcn.xyz", coord_type="redund")
geom.set_calculator(PySCF(basis="321g"))
opt_kwargs = {
"hessian_init": "fischer",
"dump": True,
"rx_coords": ((2, 1, 0), ),
"thresh": "gau_tight",
"max_line_search": True,
"min_line_search": True,
}
opt = tsopt_cls(geom, **opt_kwargs)
opt.run()
do_final_hessian(geom, write_imag_modes=True)
assert opt.is_converged
# 11 without linesearch
assert opt.cur_cycle == ref_cycle
assert geom.energy == pytest.approx(-92.2460426792319)
def test_oniom3():
run_dict = {
"xyz": "lib:oniom3alkyl.pdb",
"coord_type": "redund",
"calc": {
"type": "oniom",
"calcs": {
"real": {
"type": "pyscf",
"basis": "sto3g",
"pal": 2,
},
"mid": {
"type": "pyscf",
"basis": "321g",
"pal": 2,
},
"high": {
"type": "pyscf",
# "basis": "sto3g",
"basis": "431g",
"pal": 2,
},
},
"models": {
"high": {
"inds": list(range(7, 16)),
"calc": "high",
},
"mid": {
"inds": list(range(4, 19)),
"calc": "mid",
},
}
},
"opt": {
"thresh": "gau_tight",
},
}
res = run_from_dict(run_dict)
print()
opt = res.opt
assert opt.is_converged
assert opt.cur_cycle == 7
geom = res.opt_geom
res = do_final_hessian(geom, save_hessian=False)
nus = res.nus
assert nus[-1] == pytest.approx(3747.5594141, abs=1e-2)
assert nus[-5] == pytest.approx(3563.8997581, abs=1e-2)
def test_do_final_hessian(data_dir):
fn = data_dir / "final_geometry.xyz"
geom = geom_from_xyz_file(fn, coord_type="redund")
calc = ORCA("")
grad = np.load(data_dir / "grad.npy")
hess = np.load(data_dir / "hess.npy")
geom.hessian = hess
geom.gradient = grad
res = do_final_hessian(geom, save_hessian=False)
neg_eigvals = res.neg_eigvals
assert len(neg_eigvals) == 1
np.testing.assert_allclose(neg_eigvals[0], -0.00224392407)
def test_acetaldehyde_opt():
"""
From https://doi.org/10.1016/S0166-1280(98)00475-8
"""
geom = geom_loader("lib:acetaldehyd_oniom.xyz", coord_type="redund")
real = set(range(len(geom.atoms)))
high = [4, 5, 6]
calcs = {
"real": {
"type": "g16",
"route": "hf sto-3g"
},
"high": {
"type": "g16",
"route": "b3lyp d95v"
}
}
for key, calc in calcs.items():
calc["pal"] = 2
calc["mult"] = 1
calc["charge"] = 0
models = {
"high": {
"inds": high,
"calc": "high",
},
}
oniom = ONIOM(calcs, models, geom, layers=None)
geom.set_calculator(oniom)
opt = RFOptimizer(geom, thresh="gau_tight")
opt.run()
assert geom.energy == pytest.approx(-153.07526171)
hess_result = do_final_hessian(geom, save_hessian=False)
nus = hess_result.nus
print("wavenumbers / cm⁻¹:", nus)
assert nus[-1] == pytest.approx(3759.5872)
assert nus[-3] == pytest.approx(3560.9944)
def postprocess(self):
super().postprocess()
if self.do_hess:
print()
do_final_hessian(self.geometry)
calc = Gaussian16("PM6", pal=4)
# from pysisyphus.calculators.XTB import XTB
# calc = XTB(pal=4)
geom.set_calculator(calc)
# opt = ANCOptimizer(geom, dump=True)
opt_kwargs = {
"dump": True,
"hessian_init": "calc",
"freeze_modes": 200,
"max_cycles": 20,
"prefix": "frozen_"
}
opt = NCOptimizer(geom, **opt_kwargs)
opt.run()
do_final_hessian(geom)
# from pysisyphus.Geometry import Geometry
# from pysisyphus.tsoptimizers.RSIRFOptimizer import RSIRFOptimizer
# geom = Geometry(geom.atoms, geom.coords, coord_type="redund", define_prims=((20, 19),))
# geom.set_calculator(calc)
# tsopt = RSIRFOptimizer(geom, hessian_recalc=5, trust_max=0.3)
# tsopt.run()
# do_final_hessian(geom)
# from pysisyphus.irc.EulerPC import EulerPC
# geom = Geometry(geom.atoms, geom.cart_coords)
# geom.set_calculator(calc)
# irc = EulerPC(geom)
# irc.run()